The intrinsic conformation of a Lewis antigen: The Lewis×trisaccharide

Revisiting the structural basis for biological activity of GMI-1070, a sialyl Lewisx mimetic

When it comes to the treatment of pathologies in which aberrant cell adhesion and extravasation from the bloodstream have been implicated, the selectins represent a central therapeutic target. In this context, the present work investigates the conformational landscape of two prototypes for the design of new antineoplasic and anti-inflammatory agents: the natural selectin ligand sialyl Lewis^x and its mimetic GMI-1070. Accordingly, a series of unbiased molecular dynamics simulations at the microsecond scale using GROMOS 53A6 (GLYC), CHARMM36m and GLYCAM06 force fields were employed, together with ConfID, an analytical method for the characterization of conformational populations of small molecules. Our results for sialyl Lewis^x are in agreement with and expand upon prior work. As for the mimetic, our results indicate that, in spite of its conformational restriction, GMI-1070's behavior in solution deviates from what had been proposed, highlighting thus some features that could be optimized, as the development of sialyl Lewis^x mimetics continues, and new candidates emerge.

Carbohydrates

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Stabilization of branched oligosaccharides: Lewis(x) benefits from a nonconventional C-H···O hydrogen bond

Although animal lectins usually show a high degree of specificity for glycan structures, their single-site binding affinities are typically weak, a drawback which is often compensated in biological systems by an oligovalent presentation of carbohydrate epitopes. For the design of monovalent glycomimetics, structural information regarding solution and bound conformation of the carbohydrate lead represents a valuable starting point. In this paper, we focus on the conformation of the trisaccharide Le(x) (Gal[Fucα(1-3)]β(1-4)GlcNAc). Mainly because of the unfavorable tumbling regime, the elucidation of the solution conformation of Le(x) by NMR has only been partially successful so far. Le(x) was therefore attached to a (13)C,(15)N-labeled protein. (13)C,(15)N-filtered NOESY NMR techniques at ultrahigh field allowed increasing the maximal NOE enhancement, resulting in a high number of distance restraints per glycosidic bond and, consequently, a well-defined structure. In addition to the known contributors to the conformational restriction of the Le(x) structure (exoanomeric effect, steric compression induced by the NHAc group adjacent to the linking position of L-fucose, and the hydrophobic interaction of L-fucose with the β-face of D-galactose), a nonconventional C-H···O hydrogen bond between H-C(5) of L-fucose and O(5) of D-galactose was identified. According to quantum mechanical calculations, this C-H···O hydrogen bond is the most prominent factor in stabilization, contributing 40% of the total stabilization energy. We therefore propose that the nonconventional hydrogen bond contributing to a reduction of the conformational flexibility of the Le(x) core represents a novel element of the glycocode. Its relevance to the stabilization of related branched oligosaccharides is currently being studied.

Membrane adhesion via homophilic saccharide-saccharide interactions investigated by neutron scattering

Solid-supported membrane multilayers doped with membrane-anchored oligosaccharides bearing the LewisX motif (Le(X) lipid) were utilized as a model system of membrane adhesion mediated via homophilic carbohydrate-carbohydrate interactions. Specular and off-specular neutron scattering in bulk aqueous electrolytes allowed us to study multilayer structure and membrane mechanics at full hydration at various Ca(2+) concentrations, indicating that membrane-anchored Le(X) cross-links the adjacent membranes. To estimate forces and energies required for cross-linking, we theoretically modeled the interactions between phospholipid membranes and compared this model with our experimental results on membranes doped with Le(X) lipids. We demonstrated that the bending rigidity, extracted from the off-specular scattering signals, is not significantly influenced by the molar fraction of Le(X) lipids, while the vertical compression modulus (and thus the intermembrane confinement) increases with the molar fraction of Le(X) lipids.