Recognition and reactivity in the binding between Raf kinase inhibitor protein and its small-molecule inhibitor...

The present work is aimed to provide detail on the binding process between Raf kinase inhibitor protein (RKIP) and locostatin, the only exogenous compound known to alter the function of RKIP. Understanding the basis of RKIP inhibition for use in pharmacological applications is of considerable interest, as dysregulated RKIP expression has the potential to contribute to pathophysiological processes. Herein, we report a series of atomistic models to describe the protein-ligand recognition step and the subsequent reactivity steps. Modeling approaches include ligand docking, molecular dynamics, and quantum mechanics/molecular mechanics calculations. We expect that such a computational assay will serve to study similar complexes in which potency is associated with recognition and reactivity. Although previous data suggested a single amino acid residue (His86) to be involved in the binding of locostatin, the actual ligand conformation and the steps involved in the reactivity process remain elusive from a detailed atomistic description. We show that the first reaction step, consisting of a nucleophilic attack of the nitrogen (Nε) of His86 at the sp(2)-hybridized carbon (C2) of locostatin, presents a late transition state (almost identical to the product). The reaction is followed by a hydrogen abstraction and hydrolysis. The theoretically predicted overall rate constant (6 M(-1) s(-1)) is in a very good agreement with the experimentally determined rate constant (13 M(-1) s(-1)).