Optimization of Tether Length in Nonglycosidically Linked Bivalent Ligands That Target Sites 2 and 1 of a Shiga-like Toxin

Abstract

A series of bivalent ligands for a Shiga-like toxin have been synthesized, their experimentally determined inhibitory activities were compared with a simplified thermodynamic model, and computer simulations were used to predict the optimal tether length in bivalent ligands. The design of the inhibitors exploits the proximity of the C-2' hydroxyl groups of two P(k)-trisaccharides when bound to two different, neighboring carbohydrate recognizing binding sites located on the surface of Shiga-like toxin. NMR studies of the complex between the toxin and bivalent ligands show that site 2 and site 1 of a single B subunit are simultaneously occupied by a tethered P(k)-trisaccharide dimer. A simplified thermodynamic treatment provides the intrinsic affinities and binding energies for the intermolecular and intramolecular association events and permits the deconvolution of the contributions to the relative binding energies for the set of bivalent ligands. Conformational analysis based on MD simulations for bivalent galabioside dimers containing different tethers demonstrated that the calculated local concentrations of the pendant ligand at the second binding site correlate with the experimentally determined relative affinity values of the respective bivalent ligands, thereby providing a predictive method to optimize tether length.

Multivalency in Ligand Design

“…A more expansive collection can be found in the book by Choi [16]. 105]. This design maximizes the avidity entropy (Section 2.4.2) because the number of states for the fully associated receptor-ligand complex is at a maximum (there are more ways to arrange the receptor-ligand complex than when the ligands are bound to a rigid scaffold).…”

“…2.6) predicts a much smaller loss in conformational entropy upon complexation for long, flexible linkers than the model based on the assumption of bonds that are free rotors, which become completely restricted upon oligovalent receptor-ligand association. This C eff model has been used to rationalize the tight-binding (low values of K d avidity ) observed for oligovalent sugars tethered by flexible linkers binding to pentavalent toxins (Section 2.5.2.3) [38,105].…”

Synthesis of a αMan(1→3)αMan(1→2)αMan Glycocluster Presented on aβ‐Cyclodextrin Scaffold

“…[15] If the spatial arrangement of carbohydrate-binding sites in an oligovalent protein receptor is known then optimization of the architecture of multivalent carbohydrate ligands can lead to the design of highly efficient inhibitors. [16] However, if the identity of a natural carbohydrate ligand is not clearly established, then synthetic well-defined multivalent sugar ligands can serve as probes for elucidating the specificity of the carbohydratebinding sites of a receptor.…”

Potent and Long-Acting Dimeric Inhibitors of Influenza Virus Neuraminidase Are Effective at a Once-Weekly Dosing Regimen

“…There are numerous examples of natural multivalent interactions, many of which involve the binding of multiple copies of a carbohydrate or oligosaccharide ligand to protein receptors on a cell surface (2,3,19). Because of the importance of multivalency in biological systems, there has been a growing research effort to explore and rationalize the effects of multivalency (8,16,18) and also to make use of multivalent ligands as potentially more effective new drugs (10). Thus, a number of multivalent compounds and particularly dimeric forms of known small-molecule therapeutic agents are being investigated as drug candidates (31).…”