Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors

Abstract

Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38α keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38α in its bound state, ligand unbinding features energetically unfavorable protein–ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38α systems, providing useful information for development of inhibitors.

In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method

“…From the loading plot, it can be deduced that larger molecular volume contributes to longer residence time, while stronger hydrophilic interactions contribute to faster dissociation (Figure 7d). The result proposed in this study is consistent with previous researches, which suggested that type I kinases inhibitors bind to the ATP binding site and usually smaller and faster, while compounds of type II are generally large since occupy additional transient sub-pocket [36,37].…”

Decisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors

“…Additionally, p38α MAPK inhibitor dissociation has been investigated by simulations. For instance, dissociation pathways of type I and type II inhibitors were evaluated utilizing accelerated MD 25 and unbinding of a type II inhibitor was studied by the metadynamics approach 11 . Moreover, dissociation of selected type I and type II inhibitors were studied by steered MD 10 .…”

Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed?

“…7 It requires a well-defined reaction coordinate (RC) represented by one or a few variables. 11–13 Intensive conformational sampling is performed by enforcing external restraints at the conformations along the RC within a series of successive overlapping windows. Finally, the PMF can be constructed by removing the external restraints.…”