Szabolcs Béni

Analysis and characterization of heparin impurities

AbstractThis review discusses recent developments in analytical methods available for the sensitive separation, detection and structural characterization of heparin contaminants. The adulteration of raw heparin with oversulfated chondroitin sulfate (OSCS) in 2007–2008 spawned a global crisis resulting in extensive revisions to the pharmacopeia monographs on heparin and prompting the FDA to recommend the development of additional physicochemical methods for the analysis of heparin purity. The analytical chemistry community quickly responded to this challenge, developing a wide variety of innovative approaches, several of which are reported in this special issue. This review provides an overview of methods of heparin isolation and digestion, discusses known heparin contaminants, including OSCS, and summarizes recent publications on heparin impurity analysis using sensors, near-IR, Raman, and NMR spectroscopy, as well as electrophoretic and chromatographic separations. FigureSchematic illustrating the process for heparin impurity characterization

Heparin characterization: Challenges and solutions

Although heparin is an important and widely prescribed pharmaceutical anticoagulant, its high degree of sequence microheterogeneity and size polydispersity make molecular-level characterization challenging. Unlike nucleic acids and proteins that are biosynthesized through template-driven assembly processes, heparin and the related glycosaminoglycan heparan sulfate are actively remodeled during biosynthesis through a series of enzymatic reactions that lead to variable levels of O- and N-sulfonation and uronic acid epimers. As summarized in this review, heparin sequence information is determined through a bottom-up approach that relies on depolymerization reactions, size- and charge-based separations, and sensitive mass spectrometric and nuclear magnetic resonance experiments to determine the structural identity of component oligosaccharides. The structure-elucidation process, along with its challenges and opportunities for future analytical improvements, is reviewed and illustrated for a heparin-derived hexasaccharide.

Clickable fluorophores for biological labeling—with or without copper

The synthesis of a set of new clickable fluorophores that virtually cover the whole visible spectrum reaching the near infra-red regime is presented herein. Besides dyes that are capable of participating in classical copper catalyzed 1,3-dipolar cycloaddition reactions with the counterparting function we have also prepared dyes containing a cyclooctyne moiety, an alkyne derivative that enables copper free clicking to azides. The suitability of these dyes for fluorescent labeling of biomolecules is presented by examples on model frameworks representing major biopolymer building blocks. The versatility of these dyes is presented in cell labeling experiments as well as by labeling the azide modified surface glycans of CHO-cells either by copper catalyzed or copper-free click reaction. These dyes are expected to have a large variety of applications in (bio)orthogonal labeling schemes both in vivo and in vitro.

Comparison of GC-MS and NMR for Metabolite Profiling of Rice Subjected to Submergence Stress.

Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and (1)H NMR results was conducted for wild-type and tolerant rice varieties stressed by up to 3 days of submergence and allowed 1 day of postsubmergence recovery. Most metabolomics studies are conducted using a single analytical platform. Each platform, however, has inherent advantages and disadvantages that can influence the analytical coverage of the metabolome. In this work, a more thorough analysis of the plant stress response was possible through the use of both (1)H NMR and GC-MS. Several metabolites, such as S-methyl methionine and the dipeptide alanylglycine, were only detected and quantified by (1)H NMR. The high dynamic range of NMR, as compared with that of the GC-TOF-MS used in this study, provided broad coverage of the metabolome in a single experiment. The sensitivity of GC-MS facilitated the quantitation of sugars, organic acids, and amino acids, some of which were not detected by NMR, and provided additional insights into the regulation of the TCA cycle. The combined metabolic information provided by (1)H NMR and GC-MS was essential for understanding the complex biochemical and molecular response of rice plants to submergence.

A Non-Fluorinated Monobenzocyclooctyne for Rapid Copper-Free Click Reactions

We designed and synthesised carboxymethylmonobenzocyclooctyne (COMBO) through a four-step reaction pathway. COMBO is a new, structurally simple, non-fluorinated, and directly conjugable copper-free click reagent, which shows excellent reaction kinetics, as also evidenced by theoretical calculations. Additionally, the carboxylic acid appendage allows further conjugation to biomolecules or fluorescent labels. The utility of COMBO in bioorthogonal labelling schemes was demonstrated when a COMBO-containing fluorescent label was employed in glycan imaging of HeLa cells (metabolically modified to have azidosialic acid residues on their cell-surface glycans).

Differential metabolic regulation governed by the rice SUB1A gene during submergence stress and identification of alanylglycine by 1H NMR spectroscopy

Although the genetic mechanism of submergence survival for rice varieties containing the SUB1A gene has been elucidated, the downstream metabolic effects have not yet been evaluated. In this study, the metabolomes of Oryza sativa ssp. japonica cv. M202 and cv. M202(Sub1) were profiled using (1)H NMR spectroscopy to compare the metabolic effect of submergence stress and recovery on rice in the presence or absence of SUB1A. Significant changes were observed in the NMR resonances of compounds in pathways important for carbohydrate metabolism. The presence of SUB1A in M202(Sub1) was correlated with suppression of carbohydrate metabolism in shoot tissue, consistent with the role of SUB1A in limiting starch catabolism to fuel elongation growth. The absence of SUB1A in M202 was correlated with greater consumption of sucrose stores and accumulation of amino acids that are synthesized from glycolysis intermediates and pyruvate. Under submergence conditions, alanine, a product of pyruvate metabolism, showed the largest difference between the two varieties, but elevated levels of glutamine, glutamate, leucine, isoleucine, threonine, and valine were also higher in M202 compared with the M202(Sub1) variety. The identification and characterization of alanylglycine (AlaGly) in rice is also reported. After 3 days of submergence stress, AlaGly levels decreased significantly in both genotypes but did not recover within 1 day of desubmergence with the other metabolites evaluated. The influence of SUB1A on dynamic changes in the metabolome during complete submergence provides new insights into the functional roles of a single gene in invoking a quiescence strategy that helps stabilize crop production in submergence-prone fields.

Separation and characterization of modified pregabalins in terms of cyclodextrin complexation, using capillary electrophoresis and nuclear magnetic resonance.

The (S)-(+)-isomer of 3-isobutyl-GABA (pregabalin), the blockbuster drug in the treatment of neuropathic pain has been separated from its R isomer by cyclodextrin modified capillary zone electrophoresis (CZE) using uncoated fused-silica capillary. Derivatization of the single isomer and the racemate with tosyl- and dansyl-chloride was carried out to introduce strong UV chromophores of different size. CE-pH titrations were performed to determine the dissociation constants for both derivatives. 30 cyclodextrin (CD) derivatives as chiral agents were used at four different pH values to study the enantioseparation of the differently protonated guest molecules. The separation was optimized as a function of CD concentration, buffer type and concentration, pH and applied voltage. For the tosylated derivate the best resolution (R(s)=2.76) was found with 6-monodeoxy-6-mono-(3-hydroxy)-propylamino-beta-cyclodextrin hydrochloride (PA-beta-CD) at pH 6.8, while with the same selector at pH 7.2 enantioseparation with an R(s) value of 4.32 could be achieved for the dansylated pregabalin. At pH 2.5 for the dansylated derivative trimethylated alpha- and beta-CD systems resulted the most significant separation (R(s)=7.38 and R(s)=7.74, respectively). Experiments with dual CD systems were carried out as well. The stoichiometry of the complexes was determined using the Job plot method and resulted in a 1:1 complex in both cases. The structures of the inclusion complexes were elucidated using 2D ROESY NMR experiments.

Utility of cyclodextrins in the formulation of genistein. Part 1. Preparation and physicochemical properties of genistein complexes with native cyclodextrins

Isoflavones are suitable guest molecules for inclusion complex formation with cyclodextrins (CDs). The molecular encapsulation with CDs results in a solid, molecularly dispersed form and in a significantly improved aqueous solubility of isoflavones. Genistein, a key isoflavone constituent of Ononidis spinosae radix was found to form a supramolecular, non-covalent inclusion complex with both beta-cyclodextrin (beta-CD) and gamma-cyclodextrin (gamma-CD), while it did not form a stable complex with alpha-CD. The guest genistein was found to spatially located in the less polar cavity of cyclodextrin. The isolated binary genistein/CD complexes appeared novel crystalline lattices. The in vitro dissolution of genistein entrapped into both beta- and gamma-CD, significantly surpassed that of the plain isoflavone.

Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra

Sulfamate groups (NHSO(3)(-)) are important structural elements in the glycosaminoglycans (GAGs) heparin and heparan sulfate (HS). In this work, proton nuclear magnetic resonance (NMR) line-shape analysis is used to explore the solvent exchange properties of the sulfamate NH groups within heparin-related mono-, di-, tetra- and pentasaccharides as a function of pH and temperature. The results of these experiments identified a persistent hydrogen bond within the Arixtra (fondaparinux sodium) pentasaccharide between the internal glucosamine sulfamate NH and the adjacent 3-O-sulfo group. This discovery provides new insights into the solution structure of the Arixtra pentasaccharide and suggests that 3-O-sulfation of the heparin N-sulfoglucosamine (GlcNS) residues pre-organize the secondary structure in a way that facilitates binding to antithrombin-III. NMR studies of the GlcNS NH groups can provide important information about heparin structure complementary to that available from NMR spectral analysis of the carbon-bound protons.

Synthesis and evaluation of phosphorus containing, specific CDK9/CycT1 inhibitors.

Although there is a significant effort in the design of a selective CDK9/CycT1 inhibitor, no compound has been proven to be a specific inhibitor of this kinase so far. The aim of this research was to develop novel and selective phosphorus containing CDK9/CycT1 inhibitors. Molecules bearing phosphonamidate, phosphonate, and phosphinate moieties were synthesized. Prepared compounds were evaluated in an enzymatic CDK9/CycT1 assay. The most potent molecules were tested in cell-based toxicity and HIV proliferation assays. Selectivity of shortlisted compounds against CDKs and other kinases was tested. The best compound was shown to be a highly specific, ATP-competitive inhibitor of CDK9/CycT1 with antiviral activity.