Tibor Kožár

Lectinomics: II. A highway to biomedical/clinical diagnostics

The review assesses current status and attempts to forecast trends in the development of lectin biorecognition technology. The progressive trend is characterized scientometrically and reflects the current transient situation, when standard low-throughput lectin-based techniques are being replaced by a novel microarray-based techniques offering high-throughput of detection. The technology is still in its infancy (validation phase), but already shows promise as an efficient tool to decipher the enormous complexity of the glycocode that influences physiological status of the cell. Further enhancement in robustness and flexibility of lectin microarrays is predicted by using recombinant and artificial lectins that will render production of lectin microarrays cost-effective and more affordable. Mass spectrometry is expected to play an important role to characterize the binding profile of new lectins. Differences in glycan recognition by lectins and anti-carbohydrate antibodies are given on a molecular basis, and strong and weak points of both biorecognition molecules in diagnosis are briefly discussed.

Lectinomics I. Relevance of exogenous plant lectins in biomedical diagnostics

This review focuses on utilization of plant lectins as medical diagnostic reagents and tools. The lectin-related diagnostic is aimed at detection of several diseases connected to alteration of the glycosylation profiles of cells and at identification of microbial and viral agents in clinical microbiology. Certain lectins, proposed for or used as diagnostic tools could even recognize those cellular determinants, which are not detected by available antibodies. Broad information is presented on the lectinomics field, illustrating that lectin diagnostics might become practical alternative to antibody-based diagnostic products. In addition, the rising trend of lectin utilization in biomedical diagnostics might initiate a development of innovative methods based on better analytical technologies. Lectin microarray, a rapid and simple methodology, can be viewed as an example for such initiative. This technology could provide simple and efficient screening tools for analysis of glycosylation patterns in biological samples (cellular extracts, tissues and the whole cells), allowing thus personalized detection of changes associated with carbohydrate-related diseases.

The conformational properties of the glycosidic linkage

Abstract Stereochemical properties of the glycosidic linkage have been studied by the quantum-chemical PCILO method, using 2-methoxytetrahydropyran as a model. Calculations of the two-dimensional, conformational (Φ, Ψ) maps showed that the rotation around the C-1O-1 bond is more hindered than that around the O-1C-6 bond, and that there are differences in the shape of the energy curve for the axial and equatorial forms of 2-methoxytetrahydropyran. The observed population of the five stable conformers at equilibrium (GG:GT:TG 1 :TG 2 :TT = 70.8:6.0:19.9:2.0:1.3) is consistent with the prediction of the anomeric and exo-anomeric effects. The calculated abundance (76.8%) of the axial form of 2-methoxytetrahydropyran is comparable with experimental results (77–80%) obtained by n.m.r. measurements in non-polar solvents. The energies found for individual conformers made it possible to calculate the magnitude of the anomeric effect (3 kJ/mol) and to determine, for the first time, the values of the exo-anomeric effect for axial (6 kJ/mol) and equatorial 2-methoxytetrahydropyran (7 kJ/mol). The calculated variations of the geometry arising from rotation around the C-1O-1 bond are consistent with results obtained by statistical analysis of experimental data for α- and β-glycosides. The results obtained, indicating that the energy, geometry, and electronic structure of glycosides are largely affected by the conformation of the acetal segment, are discussed from the point of view of conformational analysis of oligo- and poly-saccharides.

2-(Substituted phenyl)amino analogs of 1-methoxyspirobrassinol methyl ether: Synthesis and anticancer activity

New analogs of indole phytoalexin 1-methoxyspirobrassinol methyl ether have been designed by replacement of its 2-methoxy group with 2-(substituted phenyl)amino group. Synthesized by spirocyclization methodology, trans- and cis-diastereoisomers of target compounds were isolated and evaluated as potential anticancer and antimicrobial agents. Their molecular geometries were refined by ab initio minimizations. Pharmacophore modeling and QSAR studies were performed in order to correlate their molecular structure and biological activity.

RAMM — A new procedure for theoretical conformational analysis of carbohydrates

Abstract The development is described of a new molecular-mechanics procedure which is designed for investigation of the molecular structure and for the prediction of minimum-energy conformations of flexible saccharide systems. In place of the optimization of energy with respect to the Cartesian coordinates of the atoms, used in conventional molecular mechanics, the minimization is carried out on internal geometrical parameters, namely, bond lengths, bond angles, and torsional angles. For this purpose, the non-derivative method of conjugate direction based on the Powell-Zangwill algorithm is used, resulting in a considerable computational advantage for large systems. Another principal feature of the procedure is the algorithm for a determination of the energetically favored orientations of pendant groups, based on a random-walk technique in a given conformation, independent of the initial starting geometry. The performance of the program RAMM using this procedure has been illustrated by comparing (ϕ, ψ) maps obtained with different approaches utilizing the MM2 set of potential functions for a model disaccharide. It is shown that the shape of the (ϕ, ψ) maps and the relative energies of conformers are significantly affected by orientation of pendant groups.

A lectin from the Chinese bird-hunting spider binds sialic acids.

The affinity to sialic acid-containing oligosaccharides of the small-animal lectin SHL-I isolated from the venom of the Chinese bird-hunting spider Selenocosmia huwena is here described for the first time. By a strategic combination of NMR techniques, molecular modeling, and data mining tools it was possible to identify the crucial amino acid residues that are responsible for SHL-Is ability to bind sialic acid residues in a specific way. Furthermore, we are able to discuss the role of the functional groups of sialic acid when bound to SHL-I. Also the impact of Pro31 in its cis- or trans-form on SHL-Is ligand affinity is of special interest, since it answers the question if Trp32 is a crucial amino acid for stabilizing complexes between SHL-I and sialic acid. SHL-I can be considered as a proper model system that provides further insights into the binding mechanisms of small-animal lectins to sialic acid on a sub-molecular level.

Theoretical studies on the conformation of saccharides. VII: Structure and stereochemistry of α- and β-D-glucopyranose in solution

The stereochemistry of d-glucopyranose has been studied theoretically in 11 solvents. The stability of the individual conformers in solution has been compared using a method in which the total energy is divided into the energy of an isolated molecule and the solvation energy. The structure and the energy of the isolated molecule have been estimated by geometry optimization using the PCILO quantum chemical method. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from calculated properties of the solute and physiochemical properties of the solvents. The influence of the solvent on rotation of the individual pendant groups and the stability of anomers have been investigated. The calculated composition of the anomeric mixture of d-glucopyranose in various solvents at 25°C (e.g., in pyridine 49% is α-anomer, in dimethyl sulfoxide 46%, and in water 32%) is in good agreement with the available experimental data and clearly demonstrates that the solvation properties of α- and β-d-glucopyranose differ. Based on the calculated abundances of anomers the magnitude of the anomeric effect has been estimated and compared with the results of corresponding calculations on other compounds.

CORRIGENDUM: Glycan and lectin microarrays for glycomics and medicinal applications

Contractgrantsponsor: SlovakVEGA; Contractgrantnumbers: 2/7053/27;2/7028/27;2/027/10;Contractgrantsponsor: SlovakAcademyof Sciences; Contractgrantnumber:ES26220120021Correspondenceto: JanTkac,DepartmentofGlycobiotechnology,CenterforGlycomics,InstituteofChemistry,SlovakAcademyofSciences,SK-845 38 Bratislava,Slovakia,E-mail: Jan.Tkac@savba.skMedicinal Research Reviews,Vol.30,No.3,581--584,2010&2010WileyPeriodicals,Inc.

Theoretical studies on the conformation of saccharides: I. Conformational flexibility of the pyranose ring

Conformations of 2-methoxytetrahydropyran as a model for the six-membered ring in aldopyranosides have been calculated by the PCILO method using the algorithm of the conjugated gradient to optimize the geometry. The calculated geometry of the fourteen basic forms of 2-methoxytetrahydropyran was found to be in agreement with the available data obtained by X-ray diffraction of pyranosides. The results indicate differences in the geometry of 2-methoxytetrahydropyran resulting from the change of the axial vs. equatorial position of the methoxyl group. These changes are particularly meaningful in the values of bond angles and they are in agreement with the anomeric and exoanomeric effects. The experimentally found differences in the energies of an axial (4C1) and equatorial (1C4) conformer, ΔG = 2.9–3.7 kJ/mol, and the dipole moment, μ = 1.20 ± 0.05 D (1D = 3.33 10−30mAs) agree well with the calculated values ΔE = 3.18 kJ/mol and = 1.18 D which, in turn, suggest that the axial conformer is preferred over the equatorial one by a ratio a:e = 78:22.