Binding of anti-prion agents to glycosaminoglycans: Evidence from electronic absorption and circular dichroism spectroscopy

Molecular Dynamics Simulation-Based Prediction of Glycosaminoglycan Interactions with Drug Molecules

Glycosaminoglycans (GAGs) are a class of long linear anionic periodic polysaccharides. Their biological activities are very broad including tissue remodeling, regulation of cell proliferation, cell migration, cell differentiation, participation in bacterial/viral infections, and immune response. They can interact with many important biomolecular partners in the extracellular matrix of the cell including small drug molecules. Recently, several GAG-bioactive small molecule complexes have been experimentally and theoretically studied. Some of these compounds in complexes with GAGs may potentially interfere with protein-GAG or peptide-GAG multimolecular systems affecting the processes of cellular differentiation or have anti-inflammatory, antiviral as well as antithrombotic effects. Although many studies have been conducted on GAG-drug complexes, the molecular mechanisms of the formation of such complexes are still poorly understood. At the same time, the complexity of their physicochemical properties renders the use of both experimental and computational methods to study these molecular systems challenging. Here, we present the molecular dynamics-based protocols successfully employed to in silico analyze GAG-small molecule interactions.

Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue-Glycosaminoglycan Interactions

Glycosaminoglycans (GAGs) are a class of periodic anionic linear polysaccharides involved in a number of biologically relevant processes in the extracellular matrix via interactions with various types of molecules including proteins, peptides and small organic molecules. The metachromatic dye methylene blue (MB) is a GAG binding agent. This molecule possesses a tricyclic, monocationic phenothiazine ring system, while the terminal methyl groups attached to the nitrogen atoms bear the most positive charges of the cation and, therefore, represent potential binding sites for negatively charged GAGs. In this study, we rigorously explored molecular mechanisms underlying these interactions for several GAG types: heparin, heparan and chondroitin sulfates. We found that GAG-MB interactions are predominantly electrostatically driven, with the particularly important role of sulfate groups. MB oligomeric stack formation was favored in the presence of GAGs. Furthermore, the impact of MB binding on the conformation of GAGs was also evaluated. The novel results allow for better quantitative analytics of GAG composition in the studied biochemical systems using MB dye as a GAG-specific marker. Our data add to the knowledge on small molecule-GAG interactions and could be potentially useful for novel developments in drug design and putative disease therapies in which GAGs are involved.

Comment on "Emissive H-Aggregates of an Ultrafast Molecular Rotor: A Promising Platform for Sensing Heparin"

For heparin sensing, Mudliar and Singh developed fluorescence and absorption spectroscopic approaches by utilizing emissive H-aggregates of thioflavin T (ThT) formed upon heparin binding. It has been proposed that the methods work not only in pure aqueous solution but also in complex biological media such as human serum. However, the optical features used to detect and quantify heparin are very sensitive to the ionic strength of the solution and completely vanish at 1.45 mM NaCl. Curiously, the authors were able to determine the heparin content of 1% serum samples containing the same level of electrolyte. In addition, the experimental conditions employed for heparin detection in serum samples were substantially modified, reducing the optical path length from 1 to 0.1 cm and increasing the dye concentration by an unknown measure. ThT shows a concentration-dependent tendency for aqueous aggregation, which markedly modifies its absorption and fluorescence properties. The authors have failed to verify that spectral characteristics of the ThT-heparin system observed in pure aqueous medium remain unchanged at higher dye concentrations and in the presence of serum components. Taking these issues into consideration, the heparin detection scheme offered for serum samples cannot be reproduced.

Computational insights into heparin-small molecule interactions: Evaluation of the balance between stacking and non-stacking binding modes

Glycosaminoglycans (GAGs), anionic periodic linear polysaccharides, are involved in a manifold of key biochemical processes ongoing in the extracellular matrix via establishing direct intermolecular interactions with diverse classes of biopolymers as well as with bioactive small molecules. Due to their acidic nature, they are capable of binding positively charged ligands, which, in turn could affect their binding with protein and peptide targets, modulating a number of physiologically important signaling pathways. Therefore, it is of great significance to improve our understanding on the molecular basis underlying GAG-small molecule interactions. In this study, we applied in silico approaches (molecular dynamics and free energy calculations) complemented with circular dichroism and absorption spectroscopy to characterize the complex formation between heparin, one of the principal members of GAG family, and twenty different cationic ligands including therapeutic drugs, alkaloids and organic dyes. In particular, the oligomerization propensity of ligands prior to heparin binding, binding free energy parameters, effects of the ionic strength are rigorously described. Based on the performed analysis, the ligands are classified into three main groups depending on their heparin binding and oligomerization properties. The computational data agree and provide rationale for the corresponding experimental findings, contributing to the general knowledge of the physico-chemical nature of ligand-GAG intermolecular interactions.

Intense chirality induction in nitrile solvents by a helquat dye monitored by near resonance Raman scattering

Chirality induction phenomena attract attention because of their relevance to intermolecular interactions encountered in living matter. Usually, such effects are weak. However, enantiomers of a [6]helquat dye were found to induce exceptionally strong chirality in several achiral solvents containing nitrile groups. This effect was observable as an intense Raman optical activity (ROA) induced in acetonitrile, acetonitrile-d3, and liquid hydrogen cyanide solvents. The observation was verified by measurement of both helquat enantiomers which provided mirror image ROA spectra. Theoretical analysis indicated that the 532 nm laser excitation light was in a near resonance with electronic transitions of the dye, which made the effect observable in very dilute solutions (1 : 200 000 helquat to nitrile ratio) and thus the phenomenon can be generally useful in analytical chemistry.

The anticancer agent ellipticine binds to glycosaminoglycans at mildly acidic pH characteristic of the extracellular matrix of tumor tissues

This communication demonstrates the pH dependent glycosaminoglycan binding of the anticancer plant alkaloid ellipticine.

Glycosaminoglycans are potential pharmacological targets for classic DNA minor groove binder drugs berenil and pentamidine

It is shown that the antiprotozoal drugs berenil and pentamidine, conventional minor groove binders of DNA, form non-covalent complexes with polyanionic glycosaminoglycans.

Quantitative analysis of anions in glycosaminoglycans and application in heparin stability studies

The sulfo groups of glycosaminoglycans contribute to their high charge densities, and are critical for the role they play in various physiological and pathophysiological processes. Unfortunately, the sulfo groups can be hydrolyzed to inorganic sulfate. Thus, it is important to monitor the presence of these sulfo groups. In addition, free anions, including chloride, sulfate and acetate, are often present in glycosaminoglycans as a result of multiple purification steps, and their presence also needs to be monitored. In this report, ion chromatography with conductivity detection is used to analyze the anions present in glycosaminoglycans, including heparin, heparan sulfate, chondroitin sulfate and dermatan sulfate. This method allows quantitation over a wide range of concentrations, affording a limit of quantitation of 0.1 ppm and a limit of detection of 0.05 ppm for most anions of interest. The stability of heparin was also studied, providing data on the formation of both sulfate and acetate anions.

Small molecule inhibitors of protein interaction with glycosaminoglycans (SMIGs), a novel class of bioactive agents with anti-inflammatory properties

BACKGROUND

Small molecule inhibitors of biologically important protein-glycosaminoglycan (GAG) interactions have yet to be identified.

METHODS

Compound libraries were screened in an assay of L-selectin-IgG binding to heparin (a species of heparan sulfate [HS-GAG]). Hits were validated, IC-50s established and direct binding of hits to HS-GAGs was investigated by incubating compounds alone with heparin. Selectivity of inhibitors was assessed in 11 different protein-GAG binding assays. Anti-inflammatory activity of selected compounds was evaluated in animal models.

RESULTS

Screening identified a number of structurally-diverse planar aromatic cationic amines. Scaffolds similar to known GAG binders, chloroquine and tilorone, were also identified. Inhibitors displayed activity also against bovine kidney heparan sulfate. Direct binding of compounds to GAGs was verified by incubating compounds with heparin alone. Selectivity of inhibitors was demonstrated in a panel of 11 heparin binding proteins, including selectins, chemokines (IL-8, IP-10), Beta Amyloid and cytokines (VEGF, IL-6). A number of selected lead compounds showed dose-dependent efficacy in peritonitis, paw edema and delayed type hypersensitivity.

CONCLUSIONS

A new class of compounds, SMIGs, inhibits protein-GAG interaction by direct binding to GAGs. Although their IC-50s were in the low micro-molar range, SMIGs binding to HS-GAGs appeared to be stable in physiological conditions, indicating high avidity binding. SMIGs may interfere with major checkpoints for inflammatory and autoimmune events.

GENERAL SIGNIFICANCE

SMIGs are a class of structurally-diverse planar aromatic cationic amines that have an unusual mode of action - inhibiting protein-GAG interactions via direct and stable binding to GAGs. SMIGs may have therapeutic potential in inflammatory and autoimmune disorders.

Analyses of protease resistance and aggregation state of abnormal prion protein across the spectrum of human prions

Prion diseases are characterized by tissue accumulation of a misfolded, β-sheet-enriched isoform (scrapie prion protein (PrP(Sc))) of the cellular prion protein (PrP(C)). At variance with PrP(C), PrP(Sc) shows a partial resistance to protease digestion and forms highly aggregated and detergent-insoluble polymers, two properties that have been consistently used to distinguish the two proteins. In recent years, however, the idea that PrP(Sc) itself comprises heterogeneous species has grown. Most importantly, a putative proteinase K (PK)-sensitive form of PrP(Sc) (sPrP(Sc)) is being increasingly investigated for its possible role in prion infectivity, neurotoxicity, and strain variability. The study of sPrP(Sc), however, remains technically challenging because of the need of separating it from PrP(C) without using proteases. In this study, we have systematically analyzed both PK resistance and the aggregation state of purified PrP(Sc) across the whole spectrum of the currently characterized human prion strains. The results show that PrP(Sc) isolates manifest significant strain-specific differences in their PK digestion profile that are only partially explained by differences in the size of aggregates, suggesting that other factors, likely acting on PrP(Sc) aggregate stability, determine its resistance to proteolysis. Fully protease-sensitive low molecular weight aggregates were detected in all isolates but in a limited proportion of the overall PrP(Sc) (i.e. <10%), arguing against a significant role of slowly sedimenting PK-sensitive PrP(Sc) in the biogenesis of prion strains. Finally, we highlight the limitations of current operational definitions of sPrP(Sc) and of the quantitative analytical measurements that are not based on the isolation of a fully PK-sensitive PrP(Sc) form.

Profiling primaquine metabolites in primary human hepatocytes using UHPLC-QTOF-MS with 13C stable isotope labeling

Therapeutic efficiency and hemolytic toxicity of primaquine (PQ), the only drug available for radical cure of relapsing vivax malaria are believed to be mediated by its metabolites. However, identification of these metabolites has remained a major challenge apparently due to low quantities and their reactive nature. Drug candidates labeled with stable isotopes afford convenient tools for tracking drug-derived metabolites in complex matrices by liquid chromatography-tandem mass spectrometry (LC-MS-MS) and filtering for masses with twin peaks attributable to the label. This study was undertaken to identify metabolites of PQ from an in vitro incubation of a 1:1 w/w mixture of (13)C(6)-PQ/PQ with primary human hepatocytes. Acquity ultra-performance LC (UHPLC) was integrated with QTOF-MS to combine the efficiency of separation with high sensitivity, selectivity of detection and accurate mass determination. UHPLC retention time, twin mass peaks with difference of 6 (originating from (13)C(6)-PQ/PQ), and MS-MS fragmentation pattern were used for phenotyping. Besides carboxy-PQ (cPQ), formed by oxidative deamination of PQ to an aldehyde and subsequent oxidation, several other metabolites were identified: including PQ alcohol, predictably generated by oxidative deamination of PQ to an aldehyde and subsequent reduction, its acetate and the alcohol's glucuronide conjugate. Trace amounts of quinone-imine metabolites of PQ and cPQ were also detected which may be generated by hydroxylation of the PQ/cPQ quinoline ring at the 5-position and subsequent oxidation. These findings shed additional light on the human hepatic metabolism of PQ, and the method can be applied for identification of reactive PQ metabolites generated in vivo in preclinical and clinical studies.

Observation of molecular inhibition and binding structures of amyloid peptides

Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.

Heparin-induced circular dichroism of chloroquine

Circular dichroism (CD) and UV/Visible absorption (UV/Vis) spectroscopy techniques were used to investigate the interaction between heparin and chloroquine, an antimalarial drug that has shown potential as an anti-prion agent. CD spectra of rac-chloroquine upon addition of heparin provide evidence of glycosaminoglycan (GAG) binding, support recent findings suggesting that interactions between heparin and antimalarial drugs are largely due to electrostatic interactions, and represent the first reported GAG-induced CD signal of a bicyclic, aromatic compound. The association constant ( approximately 10(3)M(-1)) between chloroquine and heparin was calculated from a UV titration curve and provided additional insight into the nature of the association between these two compounds.

The anticancer activity of lytic peptides is inhibited by heparan sulfate on the surface of the tumor cells

BACKGROUND

Cationic antimicrobial peptides (CAPs) with antitumor activity constitute a promising group of novel anticancer agents. These peptides induce lysis of cancer cells through interactions with the plasma membrane. It is not known which cancer cell membrane components influence their susceptibility to CAPs. We have previously shown that CAPs interact with the two glycosaminoglycans (GAGs), heparan sulfate (HS) and chondroitin sulfate (CS), which are present on the surface of most cells. The purpose of this study was to investigate the role of the two GAGs in the cytotoxic activity of CAPs.

METHODS

Various cell lines, expressing different levels of cell surface GAGs, were exposed to bovine lactoferricin (LfcinB) and the designer peptide, KW5. The cytotoxic effect of the peptides was investigated by use of the colorimetric MTT viability assay. The cytotoxic effect on wild type CHO cells, expressing normal amounts of GAGs on the cell surface, and the mutant pgsA-745, that has no expression of GAGs on the cell surface, was also investigated.

RESULTS

We show that cells not expressing HS were more susceptible to CAPs than cells expressing HS at the cell surface. Further, exogenously added heparin inhibited the cytotoxic effect of the peptides. Chondroitin sulfate had no effect on the cytotoxic activity of KW5 and only minor effects on LfcinB cytotoxicity.

CONCLUSION

Our results show for the first time that negatively charged molecules at the surface of cancer cells inhibit the cytotoxic activity of CAPs. Our results indicate that HS at the surface of cancer cells sequesters CAPs away from the phospholipid bilayer and thereby impede their ability to induce cytolysis.

Electrospray ionization mass spectrometry as a valuable tool in the characterization of novel primaquine peptidomimetic derivatives

Novel primaquine-derived antimalarials have been extensively characterized by electrospray ionization-ion trap mass spectrometry (ESI-MS). Experiments by in-source collision-induced dissociation (CID) in the nozzle- skimmer region (NSR) or by tandem-MS are shown to be most valuable tools for the physicochemical characterization of these 8-aminoquinolinic drugs that also bear the biologically relevant imidazolidin-4-one scaffold. It was possible to find parallelism between compound stability in the NSR and its reactivity towards hydrolysis at physiological pH and T. Moreover, tandem-MS fragmentation patterns were characteristic for each family, providing a means for structural distinction of isomers and allowing to find interesting correlations between the relative abundance of particular fragments and relevant structure-activity determinants, such as Charton steric parameter, v. In conclusion, this work provides solid grounds to establish ESI-MS as a key tool for the physicochemical characterization of biopharmaceuticals bearing the 8-aminoquinoline and/or the imidazolidin-4-one moieties.

Electrospray ionization-ion trap mass spectrometry study of PQAAPro and PQProAA mimetic derivatives of the antimalarial primaquine

Electrospray ionization-ion trap mass spectrometry (ESI-MS) of imidazolidin-4-one peptidomimetic derivatives of the antimalarial drug primaquine (PQ) is reported. These compounds contain the imidazolidin-4-one moiety either at the N- or the C-terminal of a dipeptide backbone, thus respectively mimicking PQ-Amino Acid-Proline (PQAAPro) and PQProAA derivatives of PQ. Both the peptidomimetics and precursors previously developed by us are promising drug candidates, as they were found to be active against rodent Plasmodium berghei malaria and Pneumocystis carinii pneumonia. Collision-induced dissociation (CID) and tandem-mass spectra (MS) of the title compounds, and fragmentation pathways thereof, led to the following findings: (1) CID patterns present some parallelism with the reactivity towards hydrolysis previously found for the same or related compounds; (2) a positional shift of the imidazolidin-4-one ring is reflected on both degree and pathways of fragmentation, which makes tandem-MS a key tool for differentiation of imidazolidin-4-one isomers; (3) the major MS/MS fragmentation of PQProAA mimetics involves release of a neutral diketopiperazine (DKP), in parallel to the "diketopiperazine pathway" described in tandem-MS studies of oligopeptides; (4) the relative abundance of a major fragment in tandem-MS spectra is inversely correlated with the size of the N-terminal AA in PQProAA mimetics. Overall, this work embodies an original and valuable contribution towards a deeper insight into the molecular properties of novel antimalarials, which can be viewed as representative of both the 8-aminoquinoline and, especially, the imidazolidin-4-one structural classes.

Structure, biological activity, and enzymatic transformation of fucoidans from the brown seaweeds

Recent advances in the study of fucoidans, biologically active sulfated alpha-L-fucans of diverse structures and synthesized exclusively by marine organisms, are overviewed. Their structure, biological activity, the products of their enzymatic degradation and the different enzymes of degradation and modification are considered.