Ganglioside GM1 mimics: lipophilic substituents improve affinity for cholera toxin

Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B

Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.

Screening of a Glycopolymer Library of GM1 Mimics Containing Hydrophobic Units Using Surface Plasmon Resonance Imaging

Effective screening methods for the development of glycopolymers as molecular recognition materials are desirable for the discovery of novel biofunctional materials. A glycopolymer library was prepared to obtain guidelines for the design of glycopolymers for the recognition of cholera toxin B subunits (CTB). Glycopolymers with varying ratios of hydrophobic and sugar units were synthesized by reversible addition fragmentation chain transfer polymerization. N-tert-Butylacrylamide, N-phenylacrylamide, and N-cyclohexylacrylamide as hydrophobic units were copolymerized in the polymer backbone, and galactose, which contributes to CTB recognition, was introduced into the side chains by "post-click" chemistry. The thiol-terminated glycopolymers were immobilized on a gold surface. The polymer immobilization substrate was analyzed in terms of interaction with galactose recognition proteins (CTB, peanut agglutinin, and Ricinus communis agglutinin I) using surface plasmon resonance imaging. The polymers with high ratios of sugar and hydrophobic units had the strongest interactions with the CTB, which was different from the trend with peanut agglutinin and Ricinus communis agglutinin I. The binding constant of the CTB with the glycopolymer with hydrophobic units was 4.1 × 10⁶ M^-1, which was approximately eight times larger than that of the polymer without hydrophobic units. A correlation was observed between the log P value and the binding constant, indicating that the hydrophobic interaction played an important role in binding. New guidelines for the design of recognition materials were obtained by our screening method.

Synthesis of 1,2,3-triazole linked galactopyranosides and evaluation of cholera toxin inhibition

We report the synthesis of a series of bivalent 1,2,3-triazole linked galactopyranosides as potential inhibitors of cholera toxin (CT). The inhibitory activity of the bivalent series was examined (ELISA) and the series showed low inhibitory activity (millimolar IC(50)s). Conversely, the monomeric galactotriazole analogues were strong inhibitors of cholera toxin (IC(50) = 71-75 μM).

Cholera toxin inhibitors studied with high-performance liquid affinity chromatography: a robust method to evaluate receptor-ligand interactions

Anti-adhesion drugs may be an alternative to antibiotics to control infection of micro-organisms. The well-characterized interaction between cholera toxin and the cellular glycolipid GM1 makes it an attractive model for inhibition studies in general. In this report, we demonstrate a high-performance liquid affinity chromatography approach called weak affinity chromatography to evaluate cholera toxin inhibitors. The cholera toxin B-subunit was covalently coupled to porous silica and a (weak) affinity column was produced. The K(D) values of galactose and meta-nitrophenyl alpha-D-galactoside were determined with weak affinity chromatography to be 52 and 1 mM, respectively, which agree well with IC(50) values previously reported. To increase inhibition potency multivalent inhibitors have been developed and the interaction with multivalent glycopolypeptides was also evaluated. The affinity of these compounds was found to correlate with the galactoside content but K(D) values were not obtained because of the inhomogeneous response and slow off-rate from multivalent interactions. Despite the limitations in obtaining direct K(D) values of the multivalent galactopolypeptides, weak affinity chromatography represents an additional and valuable tool in the evaluation of monovalent as well as multivalent cholera toxin inhibitors. It offers multiple advantages, such as a low sample consumption, high reproducibility and short analysis time, which are often not observed in other methods of analysis.

First round of a focused library of cholera toxin inhibitors

C-Galactosides have been used as scaffolds to design a library of non-hydrolysable inhibitors of cholera toxin (CT). Test elements from the library were synthesized and found to inhibit CT binding to an asialofetuin-coated SPR chip with micromolar affinity. Preliminary results are reported.

Conformations of higher gangliosides and their binding with cholera toxin - investigation by molecular modeling, molecular mechanics, and molecular dynamics

Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface higher gangliosides (GT1A and GT1B) and their interaction with Cholera Toxin. The water mediated hydrogen bonding network exists between sugar residues in gangliosides. An integrated molecular modeling, molecular mechanics, and molecular dynamics calculation of cholera toxin complexed with GT1A and GT1B reveal that, the active site of cholera toxin can accommodate these higher gangliosides. Direct and water mediated hydrogen bonding interactions stabilize these binding modes and play an essential role in defining the order of specificity for different higher ganglioside towards cholera toxin. This study identifies that the binding site of cholera toxin is shallow and can accommodate a maximum of two NeuNAc residues. The NeuNAc binding site of cholera toxin may be crucial for the design of inhibitors that can prevent the infection of cholera.

A synthetic divalent cholera toxin glycocalix[4]arene ligand having higher affinity than natural GM1 oligosaccharide

A high-affinity ligand of cholera toxin, the divalent glycocalix[4]arene 1, was obtained by exploiting a combination of structure-based design of glycomimetic monovalent ligands and affinity enhancements by multivalent presentation through a calix[4]arene scaffold. It exhibits a slightly higher affinity for the toxin than its natural ligand, the GM1 oligosaccharide.

Disialogangliosides and Their Interaction with Cholera Toxin—Investigation by Molecular Modeling, Molecular Mechanics and Molecular Dynamics

Molecular mechanics and molecular dynamics studies are performed to investigate the conformational preference of cell surface disialogangliosides (GD1A, GD1B and GD3) in aqueous environment. The molecular mechanics calculation reveals that water mediated hydrogen bonding network plays a significant role in the structural stabilization of GD1A, GD1B and GD3. These water mediated hydrogen bonds not only exist between neighboring residues but also exist between residues that are separated by 2 to 3 residues in between. The conformational energy difference between different conformational states of gangliosides correlates very well with the number of water mediated and direct hydrogen bonds. The spatial flexibility of NeuNAc of gangliosides at the binding site of cholera toxin is worked out. The NeuNAc has a limited allowed eulerian space at the binding site of Cholera Toxin (2.4%). The molecular modeling, molecular mechanics and molecular dynamics of disialoganglioside-cholera toxin complex reveal that cholera toxin can accommodate the disialoganglioside GD1A in three different modes. A single mode of binding is permissible for GD1B and GD3. Direct and water mediated hydrogen bonding interactions stabilizes these binding modes and play an essential role in defining the order of specificity for different disialogangliosides towards cholera toxin. This study not only provides models for the disialoganglioside-cholera toxin complexes but also identifies the NeuNAc binding site as a site for design of inhibitors that can restrict the pathogenic activity of cholera toxin.

Intramolecular Carbohydrate-Aromatic Interactions and Intermolecular van der Waals Interactions Enhance the Molecular Recognition Ability of GM1 Glycomimetics for Cholera Toxin

The design and synthesis of two GM1 glycomimetics, 6 and 7, and analysis of their conformation in the free state and when complexed to cholera toxin is described. These compounds, which include an (R)-cyclohexyllactic acid and an (R)-phenyllactic acid fragment, respectively, display significant affinity for cholera toxin. A detailed NMR spectroscopy study of the toxin/glycomimetic complexes, assisted by molecular modeling techniques, has allowed their interactions with the toxin to be explained at the atomic level. It is shown that intramolecular van der Waals and CH-pi carbohydrate-aromatic interactions define the conformational properties of 7, which adopts a three-dimensional structure significantly preorganized for proper interaction with the toxin. The exploitation of this kind of sugar-aromatic interaction, which is very well described in the context of carbohydrate/protein complexes, may open new avenues for the rational design of sugar mimics.