Carboxylate-based receptors for the recognition of carbohydrates in organic and aqueous media

Acyclic receptors containing neutral and ionic hydrogen-bonding sites, such as amino-pyridine and carboxylate groups, were prepared and their binding properties toward neutral sugar molecules were studied. The binding studies with disodium and bis(tetramethylammonium) salts containing the dianion 11 have revealed that this type of receptor molecule is able to recognize the selected sugars in both organic and aqueous media. The carboxylate/pyridine-based receptor 11 exhibits in chloroform at least a 100-fold higher affinity for glucopyranosides than the previously described triarmed pyridine-based receptor 1, incorporating only neutral hydrogen-bonding sites. A substantial drop in the association constants is expectedly observed for an ester analogue of 11, compound 9. The dicarboxylate 11 is able to form complexes in water with methyl beta-D-glucopyranoside and D-cellobiose, with a preference for the disaccharide. The studies show the importance of charge-reinforced hydrogen bonds in the recognition of carbohydrates.     

Highly Effective Recognition of Carbohydrates by Phenanthroline‐Based Receptors: α‐ versus β‐Anomer Binding Preference

¹H NMR spectroscopic titrations in competitive and non‐competitive media, as well as binding studies in two‐phase systems, such as phase transfer of sugars from aqueous into organic solvents and dissolution of solid carbohydrates in apolar media revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of an acyclic phenanthroline‐based receptor 1 . Compared to the previously described acyclic receptors, compound 1 displays significantly higher binding affinities, the rare capability to extract sugars from water into non‐polar organic solutions and α‐ versus β‐anomer binding preference in the recognition of glycosides, which differs from those observed for other receptor systems. X‐ray crystallographic investigations revealed the presence of water molecules in the binding pocket of 1 that are engaged in the formation of hydrogen‐bonding motifs similar to those suggested by molecular modelling for the sugar OH groups in the receptor–sugar complexes. The molecular modelling calculations, synthesis, crystal structure and binding properties of 1 are described and compared with those of the previously described receptors.     

Development of a sugar-binding residue prediction system from protein sequences using support vector machine

Several methods have been proposed for protein–sugar binding site prediction using machine learning algorithms. However, they are not effective to learn various properties of binding site residues caused by various interactions between proteins and sugars. In this study, we classified sugars into acidic and nonacidic sugars and showed that their binding sites have different amino acid occurrence frequencies. By using this result, we developed sugar-binding residue predictors dedicated to the two classes of sugars: an acid sugar binding predictor and a nonacidic sugar binding predictor. We also developed a combination predictor which combines the results of the two predictors. We showed that when a sugar is known to be an acidic sugar, the acidic sugar binding predictor achieves the best performance, and showed that when a sugar is known to be a nonacidic sugar or is not known to be either of the two classes, the combination predictor achieves the best performance. Our method uses only amino acid sequences for prediction. Support vector machine was used as a machine learning algorithm and the position-specific scoring matrix created by the position-specific iterative basic local alignment search tool was used as the feature vector. We evaluated the performance of the predictors using five-fold cross-validation. We have launched our system, as an open source freeware tool on the GitHub repository (https://doi.org/10.5281/zenodo.61513).     

Coarse‐grained molecular dynamics simulations of protein–ligand binding

Coarse‐grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. We chose two protein–ligand systems, the levansucrase–sugar (glucose or sucrose), and LinB–1,2‐dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand‐binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse‐grained (CG) ligand molecules revealed potential ligand‐binding sites on the protein surfaces other than the real ligand‐binding sites. The ligands bound most strongly to the real ligand‐binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase–sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand‐binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein–ligand binding processes. © 2014 Wiley Periodicals, Inc.     

Voltammetric detection of lectin using sugar labeled with electroactive substance.

The voltammetric detection of soybean agglutinin (SBA) was investigated on the basis of an interaction between the lectin and a sugar. Because galactose and lactose combined with SBA, the sugars were labeled by a Schiff base with an electroactive daunomycin. After the labeled sugar and SBA were mixed, measurements were carried out by voltammetry. When SBA-sugar binding occurs, a part of daunomycin of the labeled sugar is taken to the binding sites. As a result, SBA is detected by a change in the peak current of daunomycin, and the SBA-sugar interaction is evaluated. The length of the alkyl chain between daunomycin and the sugar was also considered. The electrode response to the concentration of SBA was linear over the range of 0.04-0.8 microg min(-1). The merits of this procedure are the convenient preparation of labeled sugar and a rapid measurement without separation. On the other hand, the detection of sugar at the 10(-9) mol dm(-3) level was achieved by a competitive reaction to limited binding sites of the lectin between the sugar and the labeled sugar.     

Effect of solvent polarity and viscosity on the guest binding dynamics with bile salt aggregates

Bile salts form supramolecular aggregates with two binding sites with different properties. The guest binding dynamics to the aggregates and guest protection from species in the aqueous phase were investigated using fluorescence and laser flash photolysis experiments. Sodium cholate, deoxycholate and taurodeoxycholate were used as bile salts and acetonitrile or ethylene glycol were added as co-solvents to water in order to alter the binding properties of 1-ethylnaphthalene and 1-naphthyl-1-ethanol with the aggregates. The binding dynamics are faster and protection efficiencies are lower for guests bound to cholate and in the presence of either co-solvent.     

Water Dynamics in Starch Based Confectionery Products including Different Types of Sugar

Starch-based confectionery products were prepared using different types of sugar. In addition to using different sugar, starch was replaced with soy protein isolate (SPI) in some of the products. ¹H NMR spin-lattice relaxation experiments were performed for the collection of products in a broad frequency range from 4 KHz to 30 MHz to get insight into the influence of different sugar types and SPI on the dynamics of water in composite gel systems. The relaxation data have been decomposed into relaxation contributions associated with two different pools of water molecules characterized by different mobility. The translation dynamics of water molecules has been quantitatively described in terms of a dedicated relaxation model. The influence of the sample composition (the type of sugar and/or the presence of SPI) on the water mobility was thoroughly discussed. The results indicate that the addition of soy protein does not affect water dynamics for samples including sucrose. In addition, as the complementary measurements, physical properties of the products, such as the moisture content, water activity and texture, were investigated in terms of X-ray diffraction and thermogravimetric analysis.     

Probing the basicity of regular and defect sites of alkaline earth metal oxide surfaces by BF3 adsorption: a theoretical analysis.

The basicity of regular and low-coordinate (LC) sites (steps, edges and corners) at the surface of alkaline earths with NaCl structure (MgO, CaO, SrO, and BaO) has been investigated by using BF3 as a probe molecule. B-O and B-F distances; O-B-F bond angles; B-F asymmetric stretching frequencies; O, B and F 1s core-level binding energies; and the interaction energy of adsorbed BF3 were determined by means of DFT calculations on cluster models. These adsorption properties were compared with those of complexes of BF3 with molecules with various basicities (water, ammonia, phosphine, etc.). We show that many properties of adsorbed BF3, and in particular the experimentally accessible shifts in vibrational frequency, in B and F 1s core levels, and in BF3 desorption temperature, exhibit a linear correlation with the surface basicity as measured by the vertical ionization potential of the oxide anions. On the other hand, shifts of the O 1s core level binding energy do not provide a simple way to detect surface basicity. On a given oxide surface, the differing basicities of various sites result in measurable differences in adsorption properties. This suggests the potential use of BF3 as a probe molecule for titrating LC sites on the surface of ionic oxides.     

Synthesis, evaluation, and computational studies of naphthalimide-based long-wavelength fluorescent boronic Acid reporters

Boronic acids that change fluorescence properties upon sugar binding are very useful for the synthesis of carbohydrate sensors. Along this line, boronic acids that fluoresce beyond 500 nm are especially useful. A series of boronic acid fluorescent reporter compounds based on the 4-amino-1,8-naphthalimide structure have been synthesized (1a-d) and evaluated under near physiological conditions. These compounds showed good water solubility and significant changes in fluorescence properties after binding with sugars, with the emission wavelength being at around 570 nm. Analogues in this series with different substitutions showed similar properties. We have also examined the mechanism of the observed fluorescence changes for these compounds.     

Sugar-sensitive thin films composed of concanavalin A and glycogen.

Sugar-sensitive thin films were prepared by a layer-by-layer deposition of concanavalin A (Con A) and glycogen on the surface of a quartz slide and their sugar-induced decomposition was studied. The Con A/glycogen multilayer films can be decomposed by exposing them to sugar solutions (D-glucose, D-mannose, methyl-alpha-D-glucose and methyl-alpha-D-mannose), as a result of displacement of sugar residues of glycogen from the binding sites of Con A by the free sugar added in the solution. The rate of decomposition significantly depended on the type of sugar and its concentration.     

二茂铁甲酸分子印迹聚合物的制备和识别机理、结合特性

以二茂铁甲酸（FCA）为模板,选用不同的功能单体制备了一系列分子印迹聚合物,用平衡结合实验考察了它们对模板分子的结合性能。 结果表明,以甲基丙烯酸为功能单体制得的印迹聚合物P1对模板分子有很好的选择性,特异性吸附量ΔCP为23.18 μmol/g,印迹因子IF为2.33,竞争性结合实验结果表明,P1可以将模板分子从结构类似物中分离出来。 Scatchard方程研究表明,在研究的浓度范围内聚合物中形成了一类等价的结合位点,其对模板分子的平衡离解常数K=1.94 mmol/L,最大表观结合量Cpmax=92.33 μmol/g。 研究还表明,FCA的羧基是在聚合物的孔穴中产生识别位点的功能基,模板分子上的羧基与MAA的羧基形成双重氢键作用是分子识别的主要作用力。     

Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies

By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL-disaccharide complexes in solution were deduced by NMR spectroscopy using (1)H saturation transfer difference (STD) effects and transferred (1)H,(1)H-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides β-d-Galp-(1→4)-β-D-GlcpNAc-OMe and β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/π-interactions form the basis of the protein-ligand complexes in a way characteristic of carbohydrate-protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand-protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N'-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on (1)H NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein-ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.     

Thermodynamic origin of the chiral recognition of tryptophan on teicoplanin and teicoplanin aglycone stationary phases

The D-, L-tryptophan binding and the chiral recognition properties of the teicoplanin and teicoplanin aglycone (TAG) chiral stationary phase (CSPs) were compared at various column temperatures. The solute adsorption isotherms (bi-Langmuir model) were determined for both the two CSPs using the perturbation method. It was demonstrated that the sugar units were involved in the reduction of the apparent enantioselectivity through two phenomena: (i) the inhibition of some enantioselective contacts with low-affinity binding regions of the aglycone and (ii) a decrease in the stereoselective properties of the aglycone high-affinity binding pocket. The phenomenon (ii) was governed by both a decrease in the ratio of the enantiomer adsorption constant and a strong reduction of the site accessibility for D- and L-tryptophan. In addition, a temperature effect study was performed to investigate the chiral recognition mechanism at the aglycone high-affinity pocket. An enthalpy-entropy compensation analysis derived from the Grunwald model as well as the comparison with the literature data demonstrated that the enantioselective binding mode was dependent on an interface dehydration process. The change in the enantioselective process observed between the TAG and teicoplanin CSP was characterized by a difference of ca. 2-3 ordered water molecules released from the species interface.     

Suppression of background sites in molecularly imprinted polymers via urea-urea monomer aggregation

The molecular imprinting process provides a synthetically efficient route to polymers with tailored recognition properties. However, the binding properties of the templated binding sites are often masked by the more prevalent background binding sites. Therefore, a strategy for reducing the number of background binding sites was developed and evaluated that uses functional monomer aggregation to suppress the formation of background sites. A series of imprinted and non-imprinted polymers was formed using crosslinking urea monomer and were evaluated for their ability to rebind the anionic template, tetrabutylammonium diphenyl phosphate (TBA-DPP). The urea monomer was shown to form linear hydrogen bonded aggregates in solution and in the solid state. Functional monomer aggregation in the polymerization solution was shown to dramatically reduce the numbers of background binding sites by occupying and blocking the urea recognition groups that were not bound to the template molecule. Despite the low aggregation constant of the urea monomer (3.5 M(-1) in chloroform), the number of background sites was reduced by more than 60%. We predict that this strategy of using monomers that aggregate to reduce background binding sites is a general one for MIPs and other types of polymers with tailored recognition properties. The key is to identify self-assembling monomers where the guest binding processes are stronger than the aggregation processes.     

Thermodynamic contributions of the ordered water molecule in HIV-1 protease

Binding between biomolecules is usually accompanied by the formation of direct interactions with displacement of water from the binding sites. In some cases, however, the interactions are mediated by ordered water molecules, whose effect on binding affinity and the other thermodynamic functions is unclear. In this work, we compute the contribution of one such water molecule, the strongly bound water molecule at the binding site of HIV-1 protease, to the thermodynamic properties using statistical mechanical formulas for the energy and entropy. The requisite correlation functions are obtained by molecular dynamics simulations. We find that the entropic penalty of ordering is large but is outweighed by the favorable water-protein interactions. We also find a large negative contribution from this water molecule to the heat capacity. This approach could be useful in rational drug design by estimating which bound water molecules would be most favorable to displace.     

Oxime-based receptors for mono- and disaccharides

Representatives of a new series of acyclic oxime-based receptors were prepared and their binding properties toward neutral sugar molecules studied. 1H NMR and fluorescence titrations revealed that receptors 2a and 2b, incorporating suitable positioned amine and oxime moieties, are able to form strong 1:1 complexes (Ka1 approximately 10(5) M-1) with dodecyl alpha- and beta-maltoside in chloroform solutions. Furthermore, the binding studies with beta-glucopyranoside indicated the formation of complexes with 1:1 and 1:2 receptor-monosaccharide binding stoichiometry (with overall binding constant beta2 approximately 10(5) M-2). Both hydrogen bonding and interactions of the sugar CH's with the phenyl rings of the receptor contribute to the stabilization of the receptor-sugar complexes. Molecular modeling calculations, synthesis, and binding studies are described.     

Fullerene Sugar Balls: A New Class of Biologically Active Fullerene Derivatives

Among the large variety of bioactive C₆₀ derivatives, fullerene derivatives substituted with sugar residues, that is, glycofullerenes, are of particular interest. The sugar residues are not only solubilizing groups; their intrinsic biological properties also provide additional appealing features to the conjugates. The most recent advances in the synthesis and the biological applications of glycofullerenes are summarized in the present review article with special emphasis on globular glycofullerenes, that is, fullerene sugar balls, constructed on a hexa‐substituted fullerene scaffold. The high local concentration of carbohydrates around the C₆₀ core in fullerene sugar balls is perfectly suited to the binding of lectins through the “glycoside cluster effect”, and these compounds are potential anti‐adhesive agents against bacterial infection. Moreover, mannosylated fullerene sugar balls have shown antiviral activity in an Ebola pseudotyped infection model. Finally, when substituted with peripheral iminosugars, dramatic multivalent effects have been observed for glycosidase inhibition. These unexpected observations have been rationalized by the interplay of interactions involving the catalytic site of the enzyme and non‐glycone binding sites with lectin‐like abilities.     

A new boronic acid fluorescent reporter that changes emission intensities at three wavelengths upon sugar binding

The boronic acid moiety is a very useful functional group for the preparation of sugar sensors. Along this line, water-soluble boronic acids that change fluorescent properties upon sugar binding are especially useful as reporter units in fluorescent sensors for carbohydrates. Herein, we report the discovery of a new water-soluble boronic acid (1, dibenzofuran-4-boronic acid) that exhibits unique fluorescence changes at three wavelengths upon binding with sugars under near physiological conditions.     

A molecularly imprinted polymer receptor for the enantiomeric recognition of amino acid hydantoins mimicking cooperative hydrogen bonds between nucleotide bases

Using acrylamide as hydrogen bonding functional monomer and (5R)-5-benzylhydantoin as template, a molecularly imprinted polymer was prepared in a polar solvent, which exhibited good enantiomeric recognition properties. The binding characteristics and selectivity of the polymer were evaluated by batch methods. Scatchard analysis showed that two classes of binding sites were produced in the polymer matrix and their dissociation constants were calculated to be 3.5 × 10-5mol/L and 4.3 ×10-4 mol/L, respectively, by utilizing the model of multiple independent classes of binding sites. These results were more reasonable than those obtained by Scatchard analysis , which was in agreement with the prediction of the binding characteristics of the polymer by exploring the effect of acrylamide on UV spectra of (5R)-5-benzylhydantoin. The substrate- and enantio-selectivity of the polymer was investigated. Finally, the study of effect of water on the chiral separation factor of the polymer further proved that the hy