Sugar recognition: designing artificial receptors for applications in biological diagnostics and imaging

Fluorophore-Probed Curdlan Polysaccharide Chemosensor: "Turn-On" Oligosaccharide Sensing in Aqueous Media

The ability to sense saccharides in aqueous media has attracted much attention in multidisciplinary sciences because the detection of ultrahigh concentrations of sugar chains associated with serious diseases could lead to further health promotion. However, there are notable challenges. In this study, a rhodamine-modified Curdlan (Rhod-Cur) chemosensor was synthesized that exhibited distinctive fluorescence "turn-on" responses. Rhod-Cur exhibited simultaneous sensitive and selective sensing of clinically useful acarbose with a good limit of detection (5 μM) from among those of the saccharides examined. The (chir)optical properties of Rhod-Cur were elucidated using UV/vis, fluorescence, excitation, and circular dichroism spectroscopies; lifetime measurements and morphological studies using atomic force and confocal laser scanning microscopy and dynamic light scattering techniques revealed that the fluorescence "turn-on" behavior originates from globule-to-coaggregation conversion upon insertion of the oligosaccharides in the dynamic Cur backbone.

Towards Biomimetic Recognition of Glycans by Synthetic Receptors

Carbohydrates are abundant in Nature, where they are mostly assembled within glycans as free polysaccharides or conjugated to a variety of biological molecules such as proteins and lipids. Glycans exert several functions, including protein folding, stability, solubility, resistance to proteolysis, intracellular traffic, antigenicity, and recognition by carbohydrate-binding proteins. Interestingly, misregulation of their biosynthesis that leads to changes in glycan structures is frequently recognized as a mark of a disease state. Because of glycan ubiquity, carbohydrate binding agents (CBAs) targeting glycans can lead to a deeper understanding of their function and to the development of new diagnostic and prognostic strategies. Synthetic receptors selectively recognizing specific carbohydrates of biological interest have been developed over the past three decades. In addition to the success obtained in the effective recognition of monosaccharides, synthetic receptors recognizing more complex guests have also been developed, including di- and oligosaccharide fragments of glycans, shedding light on the structural and functional requirements necessary for an effective receptor. In this review, the most relevant achievements in molecular recognition of glycans and their fragments will be summarized, highlighting potentials and future perspectives of glycan-targeting synthetic receptors.

The current progress in the use of boron as a platform for novel antiviral drug design

INTRODUCTION

Boron has attracted extensive interest due to several FDA-approved boron-containing drugs and other pharmacological agents in clinical trials. As a semimetal, it has peculiar biochemical characteristics which could be utilized in designing novel drugs against drug-resistant viruses. Emerging and reemerging viral pandemics are major threats to human health. Accordingly, we aim to comprehensively review the current status of antiviral boron-containing compounds.

AREAS COVERED

This review focuses on the utilization of boron to design molecules against viruses from two perspectives: (i) single boron atom-containing compounds acting on miscellaneous viral targets and (ii) boron clusters. The peculiar properties of antiviral boron-containing compounds and their diverse binding modes with viral targets are described in detail in this review.

EXPERT OPINION

Compounds bearing boronic acid can interact with viral targets by forming covalent or robust hydrogen bonds. This feature is valuable for combating resistant viruses. Furthermore, boron clusters can form dihydrogen bonds and bear features such as three-dimensional aromaticity, hydrophobicity, and biological stability. All these features demonstrated boron as a probable essential element with immense potential for drug design.

Analysing binding stoichiometries in NMR titration experiments using Monte Carlo simulation and resampling techniques

The application of Monte Carlo simulation and resampling techniques to analyse possible binding stoichiometries in NMR titration experiments is presented. Four simulated NMR titration experiments having complex species with 1:1, 2:1 and 1:2 stoichiometries were each analysed using a 1:1, 2:1/1:1, 1:1/1:2 and a 2:1/1:1/1:2 model as implemented in SupraFit. Each best-fit model was inspected using Monte Carlo simulation (MC), Cross Validation (CV) and a new protocol termed Reduction Analysis (RA). The results of the statistical post-processes were used to calculate characteristic descriptors that are the base of the judgment for both, the models and individual stability constants. The results indicate promising approaches to correctly identify 1:1, 2:1/1:1 and 1:1/1:2 models, however with some limitations in case of the 2:1/1:1/1:2 model. All simulations and post-processing protocols were performed with the newly presented SupraFit.

Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms

The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards β-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.

Chiral Assemblies of Planar and Achiral meta-Arylene Ethynylene Macrocycles Induced by Saccharide Recognition

We created chiral assemblies of planar and achiral macrocycles by saccharide recognition. To achieve this, we synthesized stackable meta-arylene ethynylene macrocycles consisting of pyridine-acetylene-phenol and pyridine-acetylene-aniline units. ¹H NMR, absorption, and fluorescence emission spectroscopy indicated that these macrocycles formed 1:1 and 2:1 complexes with lipophilic alkyl glycosides. The 2:1 complex of the pyridine-acetylene-phenol macrocycle showed induced circular dichroism (ICD) bands, meaning that two achiral macrocycles are arranged in an asymmetrically twisted manner. CD spectroscopy revealed that the helical sense was affected by the chirality of guest saccharides. On the other hand, strong CD bands were observed after solid-liquid extraction of native saccharides into lipophilic solvents using the pyridine-acetylene-aniline macrocycle.

Chromatographic separation of glycated peptide isomers derived from glucose and fructose

Amino groups in proteins can react with aldehyde groups in aldoses or keto groups in ketoses, e.g., D-glucose and D-fructose, yielding Schiff bases that rearrange to more stable Amadori and Heyns products, respectively. Analytical strategies to identify and quantify each glycation product in the presence of the corresponding isomer are challenged by similar physicochemical properties, impeding chromatographic separations, and by identical masses including very similar fragmentation patterns in tandem mass spectrometry. Thus, we studied the separation of seven peptide families, each consisting of unmodified, glucated, and fructated 15mer to 22mer peptides using reversed-phase (RP) and hydrophilic interaction chromatography (HILIC). In RP-HPLC using acidic acetonitrile gradients, unglycated peptides eluted ~ 0.1 to 0.8 min after the corresponding glycated peptides with four of seven peptides being baseline separated. Isomeric glucated and fructated peptides typically coeluted, although two late-eluting peptides were partially separated. Neutral eluents (pH 7.2) improved the chromatographic resolution (R_s), especially in the presence of phosphate, providing good and often even baseline separations for six of the seven isomeric glycated peptide pairs with fructated peptides eluting earlier (R_s = 0.7 to 1.5). Some glucated and unmodified peptides coeluted, but they can be distinguished by mass spectrometry. HILIC separated glycated and unmodified peptides well, whereas glucated and fructated peptides typically coeluted. In conclusion, HILIC efficiently separated unmodified and the corresponding glycated peptides, while isomeric Amadori and Heyns peptides were best separated by RP-HPLC using phosphate buffered eluents.

Turn-On Fluorescent Probe Based on a Dansyl Triarginine Peptide for Ganglioside Imaging

Gangliosides play pivotal biological roles in the animal cell membranes, and it is vital to develop fluorescent probes for imaging them. To date, various artificial receptors for ganglioside imaging have been developed; however, turn-on fluorescence imaging for gangliosides with high contrast has not been achieved. We developed a simple fluorescent probe on the basis of a dansyl triarginine peptide for turn-on ganglioside imaging on the liposome membrane. The probe bound to monosialyl gangliosides and other anionic lipids with association constants was 10⁵ M^-1, which enhanced from 6-fold to 7-fold the fluorescence intensity. Upon binding to monosialyl ganglioside-containing giant liposomes, the turn-on probe selectively enhanced the fluorescence intensity compared with the other anionic lipids. This simple peptide probe for turn-on fluorescence imaging of gangliosides would provide a novel molecular tool for chemical biology.

A Pyridine-Acetylene-Aniline Oligomer: Saccharide Recognition and Influence of this Recognition Array on the Activity as Acylation Catalyst

In order to create new functions of foldamer-type hosts, various kinds of recognition arrays are expected to be developed. Here, a pyridine-acetylene-aniline unit is presented as a new class of a saccharide recognition array. The conformational stabilities of this array were analyzed by DFT calculation, and suggested that a pyridine-acetylene-aniline oligomer tends to form a helical structure. An oligomer of this array was synthesized, and its association for octyl β-D-glucopyranoside was confirmed by ¹ H NMR measurements. UV/Vis, circular dichroism, and fluorescence titration experiments revealed its high affinity for octyl glycosides in apolar solvents (K_a =10⁴ to 10⁵  M^-1 ). This oligomer was relatively stable under basic conditions, and therefore this array was expected to be applied to the derivatization of saccharides. A 4-(dialkylamino)pyridine attached pyridine-acetylene-aniline oligomer proved to catalyze the acylation of the octyl glucoside.

Paving the Way for Practical Use of Sugar-Binding Natural Products as Lectin Mimics in Glycobiological Research

Pradimicins (PRMs) constitute an exceptional class of natural products that show Ca²⁺ -dependent recognition of d-mannose (Man). In addition to therapeutic uses as antifungal drugs, the application of PRMs as lectin mimics for glycobiological research has been attracting considerable interest, since the emerging biological roles of Man-containing glycans have been highlighted. However, only a few attempts have been made to use PRMs for glycobiological purposes. The limited use of PRMs is primarily due to the early assumption that the readily modifiable carboxyl group of PRMs is involved in Ca²⁺ binding, and thus, not available to prepare research tools. Recently, this assumption has been disproved by structural elucidation of the Ca²⁺ complex of PRMs, which paves the way for designing carboxyl group modified derivatives of PRMs for research use. This article outlines studies related to Ca²⁺ -mediated Man binding of PRMs and discusses their application for glycobiology.

Selective glucose sensing in complex media using a biomimetic receptor

Glucose is a key biomedical analyte, especially relevant to the management of diabetes. Current methods for glucose determination rely on the enzyme glucose oxidase, requiring specialist instrumentation and suffering from redox-active interferents. In a new approach, a powerful and highly selective achiral glucose receptor is mixed with a sample, l-glucose is added, and the induced CD spectrum is measured. The CD signal results from competition between the enantiomers, and is used to determine the d-glucose content. The involvement of l-glucose doubles the signal range from the CD spectrometer and allows sensitivity to be adjusted over a wide dynamic range. It also negates medium effects, which must be equal for both enantiomers. The method has been demonstrated with human serum, pre-filtered to remove proteins, giving results which closely match the standard biochemical procedures, as well as a cell culture medium and a beer sample containing high (70 mM) and low (0.4 mM) glucose concentrations respectively.

Pharmaceutical Applications of Molecular Tweezers, Clefts and Clips

Synthetic acyclic receptors, composed of two arms connected with a spacer enabling molecular recognition, have been intensively explored in host-guest chemistry in the past decades. They fall into the categories of molecular tweezers, clefts and clips, depending on the geometry allowing the recognition of various guests. The advances in synthesis and mechanistic studies have pushed them forward to pharmaceutical applications, such as neurodegenerative disorders, infectious diseases, cancer, cardiovascular disease, diabetes, etc. In this review, we provide a summary of the synthetic molecular tweezers, clefts and clips that have been reported for pharmaceutical applications. Their structures, mechanism of action as well as in vitro and in vivo results are described. Such receptors were found to selectively bind biological guests, namely, nucleic acids, sugars, amino acids and proteins enabling their use as biosensors or therapeutics. Particularly interesting are dynamic molecular tweezers which are capable of controlled motion in response to an external stimulus. They proved their utility as imaging agents or in the design of controlled release systems. Despite some issues, such as stability, cytotoxicity or biocompatibility that still need to be addressed, it is obvious that molecular tweezers, clefts and clips are promising candidates for several incurable diseases as therapeutic agents, diagnostic or delivery tools.

Molecular Basis of Mannose Recognition by Pradimicins and their Application to Microbial Cell Surface Imaging

Naturally occurring pradimicins (PRMs) show specific recognition of d-mannose (d-Man) in aqueous media, which has never been achieved by artificial small molecules. Although the Ca²⁺-mediated dimerization of PRMs is essential for their d-Man binding, the dimeric structure has yet to be elucidated, leaving the question open as to how PRMs recognize d-Man. Thus, we herein report the structural elucidation of the dimer by a combination of X-ray crystallography and solid-state NMR spectroscopy. Coupled with our previous knowledge regarding the d-Man binding geometry of PRMs, elucidation of the dimer allowed reliable estimation of the mode of d-Man binding. Based on the binding model, we further developed an azide-functionalized PRM derivative (PRM-Azide) with d-Man binding specificity. Notably, PRM-Azide stained Candida rugosa cells having mannans on their cell surface through conjugation with the tetramethylrhodamine fluorophore. The present study provides the practical demonstration that PRMs can serve as lectin mimics for use in glycobiological studies.

Hexaphenolic Rigid Cages Prepared by Self-Organization of C3 v Tridentates

Coordination cages were composed by self-organization of rigid C_{3 v}-symmetric heptaarene tridentates and Pd(II) precursors. The heptaarene framework involves one mesitylene, three phenol, and three pyridine moieties, which were connected by Suzuki coupling reactions. The treatment of the tridentates with Pd(dppp)(OTf)₂ or Pd(en)(NO₃)₂ in a 2:3 molar ratio furnished coordination cages, which was ascertained by crystallography, ¹H NMR and DOSY measurements, and ESI-TOFMS and UV-vis spectra. The cages have six phenolic hydroxy groups inside and were expected to incorporate hydrogen-bonding guest molecules such as saccharides. CD and DOSY measurements showed that octyl hexoside guests could be incorporated into the cage.

Maltodextrin recognition by a macrocyclic synthetic lectin

This carbohydrate receptor achieves high affinities in water and shows an unusual preference for α-linked maltodextrins.

Specific circularly polarized luminescence of Eu(iii), Sm(iii), and Er(iii) induced by N-acetylneuraminic acid

Sialic acid chelated with the Eu, Sm and Er ions provides distinct circularly polarized luminescence (CPL) patterns that can be used for its detection. The CPL spectra were measured using the Raman optical activity (ROA) technique.

Enantioselective carbohydrate recognition by synthetic lectins in water

Carbohydrate receptors with a chiral framework have been generated by combining a tetra-aminopyrene and a C3-symmetrical triamine via isophthalamide spacers bearing water-solubilising groups. These "synthetic lectins" are the first to show enantiodiscrimination in aqueous solution, binding N-acetylglucosamine (GlcNAc) with 16 : 1 enantioselectivity. They also show exceptional affinities. GlcNAc is bound with Ka up to 1280 M-1, more than twice that measured for previous synthetic lectins, and three times the value for wheat germ agglutinin, the lectin traditionally employed to bind GlcNAc in glycobiological research. Glucose is bound with Ka = 250 M-1, again higher than previous synthetic lectins. The results suggest that chirality can improve complementarity to carbohydrate substrates and may thus be advantageous in synthetic lectin design.

Platform Synthetic Lectins for Divalent Carbohydrate Recognition in Water

Biomimetic carbohydrate receptors ("synthetic lectins") have potential as agents for biological research and medicine. However, although effective strategies are available for "all-equatorial" carbohydrates (glucose, etc.), the recognition of other types of saccharide under natural (aqueous) conditions is less well developed. Herein we report a new approach based on a pyrene platform with polar arches extending from aryl substituents. The receptors are compatible with axially substituted carbohydrates, and also feature two identical binding sites, thus mimicking the multivalency observed for natural lectins. A variant with negative charges forms 1:2 host/guest complexes with aminosugars, with K1 >3000 m(-1) for axially substituted mannosamine, whereas a positively charged version binds the important α-sialyl unit with K1 ≈1300 m(-1) .

Bioinspired Saccharide-Saccharide Interaction and Smart Polymer for Specific Enrichment of Sialylated Glycopeptides

Abnormal sialylation of proteins is highly associated with many major diseases, such as cancers and neurodegenerative diseases. However, this study is challenging owing to the difficulty in enriching trace sialylated glycopeptides (SGs) from highly complex biosamples. The key to solving this problem relies strongly on the design of novel SG receptors to capture the sialic acid (SA) moieties in a specific and tunable manner. Inspired by the saccharide-saccharide interactions in life systems, here we introduce saccharide-based SG receptors into this study. Allose (a monosaccharide) displays specific and pH-sensitive binding toward SAs. Integrating allose units into a polyacrylamide chain generates a saccharide-responsive smart copolymer (SRSC). Such design significantly improves the selectivity of SA binding; meanwhile, this binding can be intelligently triggered in a large extent by solution polarity and pH. As a result, SRSC exhibits high-performance enrichment capacity toward SGs, even under 500-fold interference of bovine serum albumins digests, which is notably higher than conventional materials. In real biosamples of HeLa cell lysates, 180 sialylated glycosylation sites (SGSs) have been identified using SRSC. This is apparently superior to those obtained by SA-binding lectins including WGA (18 SGSs) and SNA (22 SGSs). Furthermore, lactose displays good chemoselectivity toward diverse disaccharides, which indicated the good potential of lactose-based material in glycan discrimination. Subsequently, the lactose-based SRSC facilitates the stepwise isolation of O-linked or N-linked SGs with the same peptide sequence but varied glycans by CH3CN/H2O gradients. This study opens a new avenue for next generation of glycopeptide enrichment materials.

Synthetic Receptors for the High-Affinity Recognition of O-GlcNAc Derivatives

The combination of a pyrenyl tetraamine with an isophthaloyl spacer has led to two new water-soluble carbohydrate receptors ("synthetic lectins"). Both systems show outstanding affinities for derivatives of N-acetylglucosamine (GlcNAc) in aqueous solution. One receptor binds the methyl glycoside GlcNAc-β-OMe with Ka ≈20,000 m(-1), whereas the other one binds an O-GlcNAcylated peptide with Ka ≈70,000 m(-1). These values substantially exceed those usually measured for GlcNAc-binding lectins. Slow exchange on the NMR timescale enabled structural determinations for several complexes. As expected, the carbohydrate units are sandwiched between the pyrenes, with the alkoxy and NHAc groups emerging at the sides. The high affinity of the GlcNAcyl-peptide complex can be explained by extra-cavity interactions, raising the possibility of a family of complementary receptors for O-GlcNAc in different contexts.

Synthesis and evaluation of a desymmetrised synthetic lectin: an approach to carbohydrate receptors with improved versatility

A new design for carbohydrate receptors features unmatched apolar surfaces, and could lead to selectivities for a broader range of substrates.