Biomimetic Carbohydrate‐Binding Agents (CBAs): Binding Affinities and Biological Activities

A Macrocyclic Tweezers-Shaped Receptor for the Biomimetic Recognition of the Gal(α1-3)Gal Disaccharide of the α-Gal Antigen

The Gal(α1-3)Gal is the terminal disaccharide unit of the α-Gal epitope [Gal(α1-3)Gal(β1-4)GlcNAc], an exogenous antigenic determinant with several clinical implications, found in all non-primate mammals and in several dangerous pathogens, including certain protozoa and mycobacteria. Its absence in humans makes the α-Gal epitope an interesting target for several infectious diseases. Here we present the development of a macrocyclic tweezers-shaped receptor, resulting from the combination of the structural features of two predecessors belonging to the family of diaminocarbazole receptors, which exhibits binding properties in the low millimolar range toward the Gal(α1-3)Gal disaccharide of the α-Gal antigen.

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.

Sensitive and specific detection of saccharide species based on fluorescence: update from 2016

Increasing evidence supports the critical role of saccharides in various pathophysiological steps of tumor progression, where they regulate tumor proliferation, invasion, hematogenic metastasis, and angiogenesis. The identification and recognition of these saccharides provide a solid foundation for the development of targeted drug preparations, which are however not fully understood due to their complex and similar structures. In order to achieve fluorescence sensing of saccharides, extensive research has been conducted to design molecular probes and nanoparticles made of different materials. This paper aims to provide in-depth discussion of three main topics that cover the current status of the carbohydrate sensing based on the fluorescence sensing mechanism, including a phenylboronic acid-based sensing platform, non-boronic acid entities, as well as an enzyme-based sensing platform. It also highlights efforts made to understand the recognition mechanisms and improve the sensing properties of these systems. Finally, we present the challenge of achieving high selectivity and sensitivity recognition of saccharides, and suggest possible future avenues for exploration.

Probing the Importance of Host Symmetry on Carbohydrate Recognition

The design of molecular cages with low symmetry could allow for more specific tuning of their properties and better mimic the unsymmetrical and complex environment of protein pockets. However, the added value of lowering symmetry of molecular receptors has been rarely demonstrated. Herein, C₃ - and C₁ -symmetrical cages, presenting the same recognition sites, have been synthesized and investigated as hosts for carbohydrate recognition. Structurally related derivatives of glucose, galactose and mannose were found to have greater affinity to the receptor with the lowest symmetry than to their C₃ -symmetrical analogue. According to the host cavity modelling, the C₁ symmetry receptor exhibits a wider opening than its C₃ -symmetrical counterpart, providing easier access and thus promoting guest proximity to binding sites. Moreover, our results show the high stereo- and substrate selectivity of the C₁ symmetry cage with respect to its C₃ counterpart in the recognition of sugars.

Niosomes Functionalized with a Synthetic Carbohydrate Binding Agent for Mannose-Targeted Doxorubicin Delivery

Niosomes are a potential tool for the development of active targeted drug delivery systems (DDS) for cancer therapy because of their excellent behaviour in encapsulating antitumorals and the possibility to easily functionalise their surface with targeting agents. Recently, some of us developed a synthetic carbohydrate binding agent (CBA) able to target the mannosidic residues of high-mannose-type glycans overexpressed on the surface of several cancer cell lines, promoting their apoptosis. In this article, we modified the structure of this mannose receptor to obtain an amphiphilic analogue suitable for the functionalization of doxorubicin-based niosomes. Several niosomal formulations and preparation methods were investigated deeply to finally obtain functionalized niosomes suitable for parental administration, which were stable for over six months and able to encapsulate up to 85% of doxorubicin (DOXO). In vitro studies, carried out towards triple-negative cancer cells (MDA-MB231), overexpressing high-mannose-type glycans, showed a cytotoxic activity comparable to that of DOXO but with an appreciable increment in apoptosis given by the CBA. Moreover, niosomal formulation was observed to reduce doxorubicin-induced cytotoxicity towards normal cell lines of rat cardiomyocytes (H9C2). This study is propaedeutic to further in vivo investigations that can aim to shed light on the antitumoral activity and pharmacokinetics of the developed active targeted DDS.

Biomimetic Tweezers for N-Glycans: Selective Recognition of the Core GlcNAc2 Disaccharide of the Sialylglycopeptide SGP

In recent years, glycomics have shown how pervasive the role of carbohydrates in biological systems is and how chemical tools are essential to investigate glycan function and modulate carbohydrate-mediated processes. Biomimetic receptors for carbohydrates can carry out this task but, although significant affinities and selectivities toward simple saccharides have been achieved, targeting complex glycoconjugates remains a goal yet unattained. In this work we report the unprecedented recognition of a complex biantennary sialylglycopeptide (SGP) by a tweezers-shaped biomimetic receptor, which selectively binds to the core GlcNAc₂ disaccharide of the N-glycan with an affinity of 170 μM. Because of the simple structure and the remarkable binding ability, this biomimetic receptor can represent a versatile tool for glycoscience, opening the way to useful applications.

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.

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.

Mannose-binding analysis and biological application of pradimicins

Pradimicins (PRMs) are an exceptional family of natural products that specifically bind d-mannose (Man). In the past decade, their scientific significance has increased greatly, with the emergence of biological roles of Man-containing glycans. However, research into the use of PRMs has been severely limited by their inherent tendency to form water-insoluble aggregates. Recently, we have established a derivatization strategy to suppress PRM aggregation, providing an opportunity for practical application of PRMs in glycobiological research. This article first outlines the challenges in studying Man-binding mechanisms and structural modifications of PRMs, and then describes our approach to address them. We also present our recent attempts toward the development of PRM-based research tools.

A Water Soluble Pd2 L4 Cage for Selective Binding of Neu5Ac

The sialic acid N-acetylneuraminic acid (Neu5Ac) and its derivatives are involved in many biological processes including cell-cell recognition and infection by influenza. Molecules that can recognize Neu5Ac might thus be exploited to intervene in or monitor such events. A key obstacle in this development is the sparse availability of easily prepared molecules that bind to this carbohydrate in its natural solvent; water. Here, we report that the carbohydrate binding pocket of an organic soluble [Pd2 L4 ]4+ cage could be equipped with guanidinium-terminating dendrons to give the water soluble [Pd2 L4 ][NO3 ]16 cage 7. It was shown by means of NMR spectroscopy that 7 binds selectively to anionic monosaccharides and strongest to Neu5Ac with Ka =24 M-1 . The cage had low to no affinity for the thirteen neutral saccharides studied. Aided by molecular modeling, the selectivity for anionic carbohydrates such as Neu5Ac could be rationalized by the presence of charge assisted hydrogen bonds and/or the presence of a salt bridge with a guanidinium solubilizing arm of 7. Establishing that a simple coordination cage such as 7 can already selectively bind to Neu5Ac in water paves the way to improve the stability, affinity and/or selectivity properties of M2 L4 cages for carbohydrates and other small molecules.

A Pradimicin-Based Staining Dye for Glycoprotein Detection

Pradimicin A (PRM-A) and related compounds constitute an exceptional family of natural pigments that show Ca²⁺-dependent recognition of d-mannose (Man). Although these compounds hold great promise as research tools in glycobiology, their practical application has been severely limited by their inherent tendency to form water-insoluble aggregates. Here, we demonstrate that the 2-hydroxyethylamide derivative (PRM-EA) of PRM-A shows little aggregation in neutral aqueous media and retains binding specificity for Man. We also show that PRM-EA stains glycoproteins in dot blot assays, whereas PRM-A fails to do so, owing to severe aggregation. Significantly, PRM-EA is sensitive to glycoproteins carrying high mannose-type and hybrid-type N-linked glycans, but not to those carrying complex-type N-linked glycans. Such staining selectivity has never been observed in conventional dyes, suggesting that PRM-EA could serve as a unique staining agent for the selective detection of glycoproteins with terminal Man residues.

Anion binding properties of a hollow PdL-cage

The hollow [PdL][BArF]2 complex 1 of a tetra-pyridyl (py) ligand (L) has a [Pd(py)4]2+ coordination environment. Addition of coordinating anions resulted in the formation of a neutral species with Pd(py)2(anion)2 coordination environment (12A). These species bind further to the coordinating anions in the order Cl- > N3- > Br- > I- > AcO- with Ka1 : 1 ≤ 414 M-1. With relatively non-coordinating anions 1 remains intact and displays 1 : 2 binding behaviour dominated by the 1 : 1 stoichiometry in the order NO3- (∼105 M-1) » ClO4- and BF4- (∼103 M-1). As evidenced by crystal structure data, DFT calculations and {1H-19F}-HOESY NMR with BF4-, the anions are bound by charge assisted [C-H]+···anion interactions.

Molecular Recognition of Disaccharides in Water: Preorganized Macrocyclic or Adaptive Acyclic?

When facing the dilemma of following a preorganized or adaptive design approach in conceiving the architecture of new biomimetic receptors for carbohydrates, shape-persistent macrocyclic structures were most often chosen to achieve effective recognition of neutral saccharides in water. In contrast, acyclic architectures have seldom been explored, even though potentially simpler and more easily accessible. In this work, comparison of the binding properties of two structurally related diaminocarbazolic receptors, featuring a macrocyclic and an acyclic tweezer-shaped architecture, highlighted the advantages provided by the acyclic receptor in terms of selectivity in the recognition of 1,4-disaccharides of biological interest. Selective recognition of GlcNAc2 , the core fragment of N-glycans exposed on the surface of enveloped viruses, stands as an emblematic example. NMR spectroscopic data and molecular modeling calculations were used to ascertain the differences in binding mode and to shed light on the origin of recognition efficacy and selectivity.

A Synthetic Galectin Mimic

Galectins are a galactoside specific subclass of carbohydrate binding proteins (lectins) involved in various cellular activities, certain cancers, infections, inflammations, and many other biological processes. The molecular basis for the selectivity of galectins is well-documented and revolves around appropriate interaction complementarity: an aromatic residue for C-H⋅⋅⋅π interactions and polar residues for (charge assisted) hydrogen bonds with the axial hydroxyl group of a galactoside. However, no synthetic mimics are currently available. We now report on the design and synthesis of the first galectin mimic (6), and show that it has a higher than 65-fold preference for n-octyl-β-galactoside (8) over n-octyl-β-glucoside (7) in CD2 Cl2 containing 5 % [D6 ]DMSO (with Ka ≥4500 M-1 for 6:8). Molecular modeling informed by nOe studies reveal a high degree of interaction complementarity between 6 and galactoside 8, which is very similar to the interaction complementarity found in natural galectins.

A Simple Biomimetic Receptor Selectively Recognizing the GlcNAc2 Disaccharide in Water

GlcNAc₂ is the core disaccharide fragment present in N-glycans exposed on the surface of enveloped viruses of high health concern, such as coronaviruses. Because N-glycans are directly involved in the docking of viruses to host cells, recognition of GlcNAc₂ by a biomimetic receptor may be a convenient alternative to the use of lectins to interfere with viral entry and infection. Herein, we describe a simple biomimetic receptor recognizing the methyl-β-glycoside of GlcNAc₂ in water with an unprecedented affinity of 160 μM, exceeding that of more structurally complex receptors reported in the literature. The tweezers-shaped acyclic structure exhibits marked selectivity among structurally related disaccharides, and complete discrimination between mono- and disaccharides. Molecular modelling calculations supported by NOE data provided a three-dimensional description of the binding mode, shedding light on the origin of the affinities and selectivities exhibited by the receptor.

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.

A Class of Potent Inhibitors of the HIV-1 Nucleocapsid Protein Based on Aminopyrrolic Scaffolds

The HIV-1 nucleocapsid protein 7 (NC) is a potential target for effective antiretroviral therapy due to its central role in virus replication, mainly linked to nucleic acid (NA) chaperone activity, and low susceptibility to drug resistance. By screening a compounds library, we identified the aminopyrrolic compound CN14_17, a known carbohydrate binding agent, that inhibits the NC chaperone activity in the low micromolar range. Different from most of available NC inhibitors, CN14_17 fully prevents the NC-induced annealing of complementary NA sequences. Using fluorescence assays and isothermal titration calorimetry, we found that CN14_17 competes with NC for the binding to NAs, preferentially targeting single-stranded sequences. Molecular dynamics simulations confirmed that binding to cTAR occurs preferably within the guanosine-rich single stranded sequence. Finally, CN14_17 exhibited antiretroviral activity in the low micromolar range, although with a moderate therapeutic index. Overall, CN14_17 might be the progenitor of a new promising class of NC inhibitors.

Effective Recognition of Caffeine by Diaminocarbazolic Receptors

Caffeine is a competitive inhibitor of adenosine receptors and possesses wide pharmacological activity. Artificial receptors recognizing caffeine potentially have a wide range of biomedical and industrial applications. Herein, we describe two structurally related and readily available artificial receptors: 1) a macrocyclic receptor, which binds caffeine with the unprecedented affinity of 9.3 μM, though with poor selectivity; and 2) a tweezers-like structure, showing an affinity of 26 μM and a 4.5-fold and 6-fold selectivity compared to theophylline and theobromine, respectively. Binding affinities were measured by ¹ H NMR titrations and were confirmed by isothermal titration calorimetry. The X-ray structure of the complex between caffeine and the acyclic receptor revealed the origin of the recognition, explained the selectivity, and shed light on the role of hydrogen bonding and CH-π/π-π interactions.

Allosteric Recognition of Homomeric and Heteromeric Pairs of Monosaccharides by a Foldamer Capsule

The recognition of either homomeric or heteromeric pairs of pentoses in an aromatic oligoamide double helical foldamer capsule was evidenced by circular dichroism (CD), NMR spectroscopy, and X-ray crystallography. The cavity of the host was predicted to be large enough to accommodate simultaneously two xylose molecules and to form a 1:2 complex (one container, two saccharides). Solution and solid-state data revealed the selective recognition of the α-4 C1 -d-xylopyranose tautomer, which is bound at two identical sites in the foldamer cavity. A step further was achieved by sequestering a heteromeric pair of pentoses, that is, one molecule of α-4 C1 -d-xylopyranose and one molecule of β-1 C4 -d-arabinopyranose despite the symmetrical nature of the host and despite the similarity of the guests. Subtle induced-fit and allosteric effects are responsible for the outstanding selectivities observed.

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.

A Preorganized Hydrogen-Bonding Motif for the Molecular Recognition of Carbohydrates

The choice between adaptive and preorganized architectures, or of the most effective hydrogen bonding groups to be selected, are dilemmas that supramolecular chemists must address in designing synthetic receptors for such a challenging guest as carbohydrates. In this paper, structurally related architectures featuring two alternative hydrogen bonding motifs were compared to ascertain the structural and functional origin of their binding differences and the advantages that can be expected in monosaccharide recognition. A set of structurally related macrocyclic receptors were prepared, and their binding properties were measured by NMR and ITC techniques in chloroform vs a common saccharidic target, namely, the β-octyl glycoside of D-glucose. Results showed that the diaminocarbazolic motif, recently reported as the constituting unit of highly effective receptors for saccharides in water, is a superior hydrogen bonding motif compared to the previously described diaminopyrrolic motif, which was successfully employed in molecular recognition of carbohydrates in polar organic solvents, due to intrinsic structural and functional factors, rather than to hydrophobic contributions. In addition, the occurrence of a rare example of a thermodynamic template effect exerted by the beta-glucoside has been ascertained, enhancing the synthesis outcome of the otherwise low yielding preparation of the described macrocyclic receptors.

Biomimetic carbohydrate recognition

Binding saccharides with non-covalent interactions is challenging, especially in the natural medium of water, but synthetic carbohydrate receptors can be surprisingly effective.

Carbohydrate supramolecular chemistry: beyond the multivalent effect

(Hetero)multivalency acts as a multichannel switch that shapes the supramolecular properties of carbohydrates in an intrinsically multifactorial biological context.

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.