The design, synthesis and evaluation of high affinity macrocyclic carbohydrate inhibitors

Abstract

Carbohydrate–protein interactions have been investigated for a model system of a monoclonal antibody, SYA/J6, which binds a trisaccharide epitope of the O-polysaccharide of the Shigella flexneri variant Y lipopolysaccharide. The thermodynamics of binding for the methyl glycoside of the native trisaccharide epitope, Rha-Rha-GlcNAc (1) to SYA/J6 over a range of temperatures exhibits strong, linear enthalpy–entropy compensation and a negative heat capacity change (ΔC_p = −152 cal mol⁻¹ degree⁻¹). At 293 K the free energy of association is the sum of favourable enthalpy and entropy contributions (ΔH = −3.9 kcal mol⁻¹ and −TΔS = −2.9 kcal mol⁻¹). Crystal structures for SYA/J6 Fab detailed the position of the native trisaccharide epitope, Rha-Rha-GlcNAc (1), and facilitated a strategy to design a tighter binding, low molecular weight ligand. This involved pre-organization of the native trisaccharide 1 in its bound conformation by addition of intramolecular constraints (a β-alanyl or glycinyl tether). ELISA measurements indicated that the glycinyl tethered trisaccharide 2 was not an optimal candidate for further analysis, while microcalorimetry provided data showing that the β-alanyl tethered trisaccharide 3 displayed a 15-fold increase in affinity for SYA/J6. Tethering of 3 resulted in a favourable entropic contribution to binding, relative to the native trisaccharide 1 (−TΔΔS = −1.2 kcal mol⁻¹). Potential energy and dynamics calculations using the AMBER Plus force fields indicated that trisaccharide 3 adopted a rigid conformation similar to that of the bound conformation of the native trisaccharide epitope. While this strategy resulted in modest free energy gains by minimizing losses due to conformational entropy, thermodynamic data are consistent with significant contributions from solvent reorganization.