Structural investigation of multivalent carbohydrate–protein interactions using synthetic biomolecules

Synthesis of Dual-Responsive Amphiphilic Glycomacromolecules: Controlled Release of Glycan Ligands via pH and UV Stimuli

This work presents a versatile strategy for the synthesis of dual stimuli-responsive amphiphilic glycomacromolecules with tailored release properties. Amphiphilic precision glycomacromolecules (APGs) derived from tailor-made building blocks using solid phase polymer synthesis form glycofunctionalized micelles, a versatile class of materials with applications in drug delivery, as antiinfection agents as well as simple cell mimetics. In this work, this concept is extended by integrating cleavable building blocks into APGs now allowing stimuli-responsive release of glycan ligands or destruction of the micelles. This study incorporates a newly designed acid-labile building block, 4-(4-(((((9H-fluoren-9-yl)methoxy)carbonyl)amino)methyl)-1,3-dioxolan-2-yl)benzoic acid (DBA), suitable also for other types of solid phase or amide chemistry, and an established UV-cleavable 2-nitrobenzyl linker (PL). The results demonstrate that both linkers can be cleaved independently and thus allow dual stimuli-responsive release from the APG micelles. By choosing the APG design e.g., placing the cleavable linkers between glycomacromolecular blocks presenting different types of carbohydrates, they can tune APG and micellar stability as well as the interaction and cluster formation with a carbohydrate-recognizing lectin. Such dual-responsive glycofunctionalized micelles have wide potential for use in drug delivery applications or for the development as anti-adhesion agents in antiviral and antibacterial treatments.

The influence of the size of aromatic monomers on the structure and catalytic activity of polymer solid acids

High activity hyper-crosslinked polymer solid acids (HCPSAs) were prepared from different aromatic monomers, and the structure was regulated by selecting the type and size of aromatic monomers.

Targeting cancer via Golgi α-mannosidase II inhibition: How far have we come in developing effective inhibitors?

Dysregulation of glycosylation pathways has been well documented in several types of cancer, where it often participates in cancer development and progression, especially cancer metastasis. Hence, inhibition of glycosidases such as mannosidases can disrupt the biosynthesis of glycans on cell surface glycoproteins and modify their role in carcinogenesis and metastasis. Several reviews have delineated the role of N-glycosylation in cancer, but the data regarding effective inhibitors remains sparse. Golgi α-mannosidase has been an attractive therapeutic target for preventing the formation of ß1,6-branched complex type N-glycans. However, due to its high structural similarity to the broadly specific lysosomal α-mannosidase, undesired co-inhibition occurs and this leads to serious side effects that complicates its potential role as a therapeutic agent. Even though extensive efforts have been geared towards the discovery of effective inhibitors, no breakthrough has been achieved thus far which could allow for their use in clinical settings. Improving the specificity of current inhibitors towards Golgi α-mannosidase is requisite in progressing this class of compounds in cancer chemotherapy. In this review, we highlight a few potent and selective inhibitors discovered up to the present to guide researchers for rational design of further effective inhibitors to overcome the issue of specificity.

"Surface Density of Ligands Controls In-Plane and Aggregative Modes of Multivalent Glycovesicle-Lectin Recognitions"

Glycovesicles are ideal tools to delineate finer mechanisms of the interactions at the biological cell membranes.  Multivalency forms the basis which, in turn, should surpass more than one mechanism in order to maintain multiple roles that the ligand-lectin interactions encounter.  Ligand densities hold a prime control to attenuate the interactions.  In the present study, mannose trisaccharide interacting with a cognate receptor, namely, Con A, is assessed at the vesicle surfaces.  A synthetic (1→3)(1→6)-branched mannose trisaccharide is tethered with a diacetylene monomer and glycovesicles of varying sugar densities are prepared.  The polydiacetylene vesicles are prepared by maintaining uniform lipid concentrations.  The interactions of the glycovesicles with the lectin are probed through dynamic light scattering and UV-Vis spectroscopy techniques.  Binding efficacies are assessed by surface plasmon resonance technique.  Aggregative and in-plane modes of interactions follow a ligand density-dependant manner at the vesicle surface. Vesicles with sparsely populated ligands engage lectin in an aggregative mode (trans-), leading to a cross-linked complex formation.  Whereas glycovesicles imbedded with dense ligands engage lectin interaction in an in-plane mode  intramolecularly (cis-).  Sub-nanomolar dissociation constants govern the intramolecular interaction occurring within the plane of the vesicle, relatively more efficacious than the aggregative intermolecular interactions.

Directed Evolution of 2'-Fluoro-Modified, RNA-Supported Carbohydrate Clusters That Bind Tightly to HIV Antibody 2G12

Carbohydrate binding proteins (CBPs) are attractive targets in medicine and biology. Multivalency, with several glycans binding to several binding pockets in the CBP, is important for high-affinity interactions. Herein, we describe a novel platform for design of multivalent carbohydrate cluster ligands by directed evolution, in which serum-stable 2'-fluoro modified RNA (F-RNA) backbones evolve to present the glycan in optimal clusters. We have validated this method by the selection of oligomannose (Man₉) glycan clusters from a sequence pool of ∼10¹³ that bind to broadly neutralizing HIV antibody 2G12 with 13 to 36 nM affinities.

Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor

The cation-independent mannose 6-phosphate receptor (CI-MPR, IGF2 receptor or CD222), is a multifunctional glycoprotein required for normal development. Through the receptor's ability to bind unrelated extracellular and intracellular ligands, it participates in numerous functions including protein trafficking, lysosomal biogenesis, and regulation of cell growth. Clinically, endogenous CI-MPR delivers infused recombinant enzymes to lysosomes in the treatment of lysosomal storage diseases. Although four of the 15 domains comprising CI-MPR's extracellular region bind phosphorylated glycans on lysosomal enzymes, knowledge of how CI-MPR interacts with ~60 different lysosomal enzymes is limited. Here, we show by electron microscopy and hydroxyl radical protein footprinting that the N-terminal region of CI-MPR undergoes dynamic conformational changes as a consequence of ligand binding and different pH conditions. These data, coupled with X-ray crystallography, surface plasmon resonance and molecular modeling, allow us to propose a model explaining how high-affinity carbohydrate binding is achieved through allosteric domain cooperativity.

[Synthetic Studies on Developments for Bioactive New Leads of Oligovalent Symmetrical Molecules]

Interactions between carbohydrate-containing glycoproteins, proteoglycans, and glycolipids on the cell surface are important biological stages for the processes of bacterial or viral infection and tumor metastasis. Moreover, supramolecular interaction by macromolecules with two-fold (C₂) or three-fold (C₃) geometry is one of the common interactions in many important biological responses. To develop new multivalent symmetrical bioactive compounds or leads, we designed and synthesized several new molecules with these geometries and evaluated their bioactivities in an attempt to find new types of bioactive leads that may interfere with the sugar recognition process. We evaluated bioactivities including antibacterial, antiviral, and anticancer activities of targeted molecules in vitro using biological assay systems. Among the synthesized target derivatives examined, some bivalent symmetrical derivatives showed high levels of bioactivities. In this review, the author describes the results of synthesis of oligovalent symmetrical target compounds and some interesting guiding results of evaluation of their biological activities and structure-activity relationships.

Anti-proliferative Activities of Some Bivalent Symmetrical 5-Substituted Hydantoin Derivatives towards Human Brain Glioma U251 Cells (U251) and Human Carcinoma Cells (KB3-1)

Novel bivalent twin-drug type hydantoin derivatives were evaluated in vitro using a human brain glioma cell line (U251) and a human carcinoma cell line (KB3-1). Among the 5-substituted hydantoin derivatives (1a-b and 2a-d) examined in this study, bivalent symmetrical 5-substituted hydantoin derivative 1b showed the highest anti-proliferative activity towards both U251 and KB3-1 cells. The values of anti-proliferative activity (IC₅₀) of this hydantoin derivative against the two cell lines (U251 and KB3-1) were 0.46 and 5.21 µM, respectively. The anti-proliferative activity of all of the compounds except for compounds 2a and 2d against U251 cells was higher than that of cisplatin. Bivalent symmetrical compound 1b had a biphenylmethane linker in the molecule. All of the tested bivalent hydantoin derivatives showed higher activity against U251 cells than against KB3-1 cells. For twin-drug type hydantoin derivatives 2a-d, which have a linear methylene linker in the molecules, it was found that methylene linker length in these molecules have an effect on the anti-proliferative activity against U251 and KB3-1 cells.

Precipitation-free high-affinity multivalent binding by inline lectin ligands

Multivalent ligand-protein interactions are a key concept in biology mediating, for example, signalling and adhesion. Multivalent ligands often have tremendously increased binding affinities. However, they also can cause crosslinking of receptor molecules leading to precipitation of ligand-receptor complexes. Plaque formation due to precipitation is a known characteristic of numerous fatal diseases limiting a potential medical application of multivalent ligands with a precipitating binding mode. Here, we present a new design of high-potency multivalent ligands featuring an inline arrangement of ligand epitopes with exceptionally high binding affinities in the low nanomolar range. At the same time, we show with a multi-methodological approach that precipitation of the receptor is prevented. We distinguish distinct binding modes of the ligands, in particular we elucidate a unique chelating binding mode, where four receptor binding sites are simultaneously bridged by one multivalent ligand molecule. The new design concept of inline multivalent ligands, which we established for the well-investigated model lectin wheat germ agglutinin, has great potential for the development of high-potency multivalent inhibitors as future therapeutics.

Catechol-functionalized sequence-defined glycomacromolecules as covalent inhibitors of bacterial adhesion

Herein, we present the synthesis of catechol functionalized sequence-defined glycomacromolecules that can covalently block the binding site of lectins and bacterial adhesins.

Influence of the reducing-end anomeric configuration of the Man9 epitope on DC-SIGN recognition

The anomeric configuration of the reducing end of Man₉ does not influence the binding to DC-SIGN.

Assembly of Divalent Ligands and Their Effect on Divalent Binding to Pseudomonas aeruginosa Lectin LecA

Divalent ligands were prepared as inhibitors for the adhesion protein of the problematic Pseudomonas aeruginosa pathogen. Bridging two binding sites enables simultaneous binding of two galactose moieties, which strongly enhances binding. An alternating motif of glucose and triazole and aryl groups was shown to have the right mix of rigidity, solubility, and ease of synthesis. Spacers were varied with respect to the core unit as well as the aglycon portions in an attempt to optimize dynamics and enhance interactions with the protein. Affinities of the divalent ligands were measured by ITC, and K_d’s as low as 12 nM were determined, notably for a compounds with either a rigid (phenyl) or flexible (butyl) unit at the core. Introducing a phenyl aglycon moiety next to the galactoside ligands on both termini did indeed lead to a higher enthalpy of binding, which was more than compensated by entropic costs. The results are discussed in terms of thermodynamics and theoretical calculations of the expected and observed multivalency effects.

Multivalent Carbohydrate-Functionalized Polymer Nanocrystals

Nanoparticles with a covalently bound shell of carbohydrate or sulfate groups, respectively, and a polyethylene core were generated by Ni(II)-catalyzed aqueous copolymerization of ethylene with comonomers undec-10-en-1-yl sulfate, undec-10-en-1-yl β-d-glucoside or undec-10-en-1-yl α-d-mannoside, respectively. Via remote substituents of the catalyst, the degree of branching and consequently degree of crystallinity of the polyethylene core of the glyconanoparticles could be controlled. This in turn impacts particle shapes, from spherical to anisotropic platelets, as observed by cryo-transmission electron microscopy. Enzyme-linked lectin assays revealed the mannose-decorated nanocrystals to be efficient multivalent ligands for concavalin A.

Constrained saccharides: a review of structure, biology, and synthesis

Review primarily covers from 1995-2018Carbohydrate function, recognized in a multitude of biological processes, provides a precedent for developing carbohydrate surrogates that mimic the structure and function of bioactive compounds. In order to constrain highly flexible oligosaccharides, synthetic tethering techniques like those exemplified by stapled peptides are utilized to varying degrees of success. Naturally occurring constrained carbohydrates, however, exist with noteworthy cytotoxic and chemosensitizing properties. This review highlights the structure, biology, and synthesis of this intriguing class of molecules.

Selective Binders of the Tandem Src Homology 2 Domains in Syk and Zap70 Protein Kinases by DNA-Programmed Spatial Screening

Members of the Syk family of tyrosine kinases arrange Src homology 2 (SH2) domains in tandem to allow the firm binding of immunoreceptor tyrosine-based interaction motifs (ITAMs). While the advantages provided by the bivalency enhanced interactions are evident, the impact on binding specificity is less-clear. For example, the spleen tyrosine kinase (Syk) and the ζ-chain-associated protein kinase (ZAP-70) recognize the consensus sequence pYXXI/L(X)_6-8 pYXXI/L with near-identical nanomolar affinity. The nondiscriminatory recognition, on the one hand, poses a specificity challenge for the design of subtype selective protein binders and, on the other hand, raises the question as to how differential activation of Syk and ZAP-70 is ensured when both kinases are co-expressed. Herein, we identified the criteria for the design of binders that specifically address either the Syk or the Zap-70 tSH2 domain. Our approach is based on DNA-programmed spatial screening. Tyrosine-phosphorylated peptides containing the pYXXI/L motif were attached to oligonucleotides and aligned in tandem on a DNA template by means of nucleic acid hybridization. The distance between the pYXXI/L motifs and the orientation of strands were varied. The exploration exposed remarkably different recognition characteristics. While Syk tSH2 has a rather broad substrate scope, ZAP-70 tSH2 required a proximal arrangement of the phosphotyrosine ligands in defined strand orientation. The spatial screen led to the design of mutually selective, DNA-free binders, which discriminate Zap-70 and Syk tSH2 by 1 order of magnitude in affinity.

Photoinactivation of multidrug resistant bacteria by monomeric methylene blue conjugated gold nanoparticles

Multidrug resistant (MDR) bacterial infections have become a severe threat to the community health due to a progressive rise in antibiotic resistance. Nanoparticle-based photodynamic therapy (PDT) is increasingly been adopted as a potential antimicrobial option, yet the cytotoxicity associated with PDT is quite unspecific. Herein, we show Concanavalin-A (ConA) directed dextran capped gold nanoparticles (GNP_DEX-ConA) enhanced the efficacy and selectivity of methylene blue (MB) induced killing of multidrug resistant clinical isolates. Here, we show that our complex MB@GNP_DEX-ConA is effective against range of MDR clinical isolates, including Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae. In our treatment modality negligible dark toxicity suggests photochemically driven process with 97% killing of MDR bacteria. GNP_DEX-ConA with monomeric form of MB departs maximum fluorescence decay time (τf: 1.7ns in HSA) and singlet oxygen (ΔΦ; 0.84) for improved activity in albumin rich infection sites. Further, the complex show least toxicity when tested against HEK293 mammalian cells. The principle component analysis (PCA) and confocal microscopy illustrates cytosolic ¹O₂ mediated type-II PDT as mechanism of action. Hence, MB@GNP_DEX-ConA mediated PDT is potential therapeutic approach against MDR infections and can be tailored to fight other infectious diseases.

Sequence-Controlled Glycopolymers via Step-Growth Polymerization of Precision Glycomacromolecules for Lectin Receptor Clustering

A versatile approach for the synthesis of sequence-controlled multiblock copolymers, using a combination of solid phase synthesis and step-growth polymerization by photoinduced thiol-ene coupling (TEC) is presented. Following this strategy, a series of sequence-controlled glycopolymers is derived from the polymerization of a hydrophilic spacer macromonomer and different glycomacromonomers bearing between one to five α-d-Mannose (Man) ligands. Through the solid phase assembly of the macromonomers, the number and positioning of spacer and sugar moieties is controlled and translates into the sequence-control of the final polymer. A maximum M̅_n of 16 kDa, corresponding to a X̅_n of 10, for the applied macromonomers is accessible with optimized polymerization conditions. The binding behavior of the resulting multiblock glycopolymers toward the model lectin Concanavalin A (ConA) is studied via turbidity assays and surface plasmon resonance (SPR) measurements, comparing the ability of precision glycomacromolecules and glycopolymers to bind to and cross-link ConA in dependence of the number of sugar moieties and overall molecular weight. The results show that there is a clear correlation between number of Man ligands and Con A binding and clustering, whereas the length of the glycooligomer- or polymer backbone seems to have no effect.

C-Glycopyranosyl Arenes and Hetarenes: Synthetic Methods and Bioactivity Focused on Antidiabetic Potential

This Review summarizes close to 500 primary publications and surveys published since 2000 about the syntheses and diverse bioactivities of C-glycopyranosyl (het)arenes. A classification of the preparative routes to these synthetic targets according to methodologies and compound categories is provided. Several of these compounds, regardless of their natural or synthetic origin, display antidiabetic properties due to enzyme inhibition (glycogen phosphorylase, protein tyrosine phosphatase 1B) or by inhibiting renal sodium-dependent glucose cotransporter 2 (SGLT2). The latter class of synthetic inhibitors, very recently approved as antihyperglycemic drugs, opens new perspectives in the pharmacological treatment of type 2 diabetes. Various compounds with the C-glycopyranosyl (het)arene motif were subjected to biological studies displaying among others antioxidant, antiviral, antibiotic, antiadhesive, cytotoxic, and glycoenzyme inhibitory effects.

Precision Synthesis of Alternating Copolymers via Ring-Opening Polymerization of 1-Substituted Cyclobutenes

Investigation of complex molecular systems depends on our ability to correlate physical measurements with molecular structure. Interpretation of studies that rely on synthetic polymers is generally limited by their heterogeneity; i.e., there is variation in the number and arrangement of the monomeric building blocks that have been incorporated. Superior physics and biology can be performed with materials and tools that exert precise control over the sequence and spacing of functional groups. An interest in functional ligands combined with a desire to control the orientation and stereochemistry of monomer incorporation led to the design of new substrates for ruthenium-catalyzed ring-opening metathesis polymerization (ROMP). We discovered that ROMP of cyclobutene-1-carboxamides provides uniform and translationally invariant polymers. In contrast, cyclobutene-1-carboxylate esters ring open upon treatment with ruthenium catalyst, but they are stable to homopolymerization. However, in the presence of cyclohexene monomers, they undergo alternating ROMP (AROMP or alt-ROMP) to give copolymers with a precisely controlled sequence. The alternating cyclobutene ester/cyclohexene pair provides access to functional group spacing larger than is possible with homopolymers. This can be desirable; for example, polymers with a regular 8-10 Å backbone spacing of cationic charge and with between four and eight cationic groups were the most effective antibacterial agents and had low cytotoxicity. Moreover, the AROMP chemistry allows alternation of two functional moieties: one associated with the cyclohexene and one attached to the cyclobutene. In the case of antibacterial copolymers, the alternating chemistry allowed variation of hydrophobicity via the cyclohexene while maintaining a constant cation spacing through the cyclobutene. In the case of copolymers that bear donor and acceptor groups, strict alternation of the groups increased intrachain charge transfer. Like cyclobutene-1-carboxylate esters, bicyclo[4.2.0]oct-7-ene-7-carboxylate esters ring open upon treatment with ruthenium catalyst and undergo ring opening cross-metathesis with cyclohexene to form alternating copolymers. The corresponding bicyclo[4.2.0]oct-7-ene-7-carboxyamides isomerize to the bicyclo[4.2.0]oct-1(8)-ene-8-carboxamides before they can ring open. However, the isomerized amides undergo ruthenium-catalyzed ring opening metathesis and rapidly AROMP with cyclohexene. Our alternating copolymer systems allow functionality to be placed along a polymer chain with larger than typical spacing. We have used both homopolymers and alternating copolymers for defining the functional group density required for targeting a cell surface and for the exploration of functional group positioning within a polymer chain. These polymer systems provide access to new materials with previously inaccessible types of nanoscale structures.

Glyconanosynthons as powerful scaffolds and building blocks for the rapid construction of multifaceted, dense and chiral dendrimers

The arsenal of available carbohydrates can be manipulated to provide versatile building blocks toward the syntheses of complex and chiral dendrimers.