Theoretical Analysis of Bivalent Binding Avidity and Kinetics: Implications for DNA-Encoded Libraries

This study presents a theoretical framework for understanding the binding behavior of bivalent molecules—entities with two linked ligands—to immobilized targets. Bivalent molecules demonstrate increased binding compared to monovalent counterparts due to an avidity effect arising from the enhanced local concentration of the second ligand upon the first ligand's attachment. Our findings indicate that a shorter tether between ligands increases equilibrium bivalent binding, provided the short tether can span adjacent binding sites without strain. However, shorter tethers may also prolong the search for closely spaced targets, delaying equilibrium to an impractical degree. We propose a theoretical model to evaluate the equilibrium and kinetic parameters of bivalent binding, to enable optimal design of bivalent DNA-Encoded Libraries, and to effect highly efficient DNA-Encoded library (DEL) selection processes.