Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States

There is increasing interest in the discovery of small-molecule inhibitors that form covalent bonds with their targets for therapeutic applications. Nevertheless, identifying clear rational design principles remains challenging because the action of these molecules cannot be understood as common noncovalent inhibitors. Conventional kinetic models often reduce the binding of covalent inhibitors to a two-step irreversible process, overlooking rapid complex dynamics of the associated unlinked inhibitor before the formation of the covalent bond with its target. In the present analysis, we expand the intermediate state into two conformations-reactive (E.I) and nonreactive (E..I). To illustrate the consequences of such simplification, the expanded kinetic model can be reduced to an effective two-step scheme expressed in terms of the equilibrium probability of the unlinked inhibitor to form either conformation. A mass-action-based numerical workflow is implemented to simulate time-dependent kinetics, overcoming the common limitations of empirical models. The numerical workflow helps relate microscopic states observed in molecular dynamics simulations to macroscopic observables like ${\text{EC}}_{50}$ and the apparent rate of covalent inhibition, showing the impact of transient intermediates on dissociation rates and potency. The proposed framework refines the interpretation of dose-response data, aiding medicinal chemists in optimizing covalent inhibitors and provides a quantitative platform for relating molecular conformational distributions to empirical parameters.