Simplified models for heterobivalent ligand binding: when are they applicable and which are the factors that affect their target residence time

Abstract

Bivalent ligands often display high affinity/avidity for and long residence time at their target. Thereto responsible is the synergy that emanates from the simultaneous binding of their two pharmacophores to their respective target sites. Thermodynamic cycle models permit the most complete description of the binding process, and thereto, corresponding differential equation-based simulations link the “microscopic” rate constants that govern the individual binding steps to the “macroscopic” bivalent ligand’s binding properties. Present simulations of heterobivalent ligand binding led to an appreciably simpler description thereof. The thermodynamic cycle model can be split into two pathways/lanes that the bivalent ligand can solicit to reach fully bound state. Since the first binding event prompts the still free pharmacophore to stay into “forced proximity” of its target site, such lanes can be looked into by the equations that also apply to induced fit binding mechanisms. Interestingly, the simplest equations apply when bivalency goes along with a large gain in avidity. The overall bivalent ligand association and dissociation will be swifter than via each lane apart, but it is the lane that allows the fastest bidirectional “transit” between the free and the fully bound target that is chiefly solicited. The bivalent ligand’s residence time is governed not only by the stability of the fully bound complex but also by the ability of freshly dissociated pharmacophores to successfully rebind. Hence, the presence of a slow-associating pharmacophore could be counterproductive. Yet, a long residence time is unfortunately also responsible for the slow attainment of binding equilibrium.