Exploring the Protein-Ligand Paths in Aurora A/B Kinases with Enhanced Molecular Dynamics Simulations

Abstract

The unbinding of drugs from their receptors can take several minutes to hours, and this is measured by the dissociation constant (koff) and the residence time (RT=1/koff). Therefore, in order to study these events in a computational time scale and describe them at molecular level, it is necessary to use computational techniques such as molecular dynamics (MD) simulations and advanced techniques of conformational space sampling that can accelerate the exploration of these events by the incorporation of bias to the system. Well-Temperated Metadynamics (WT-Metad) is an enhanced sampling method that has been used in different studies to explore the drug's unbinding pathways and measure the free energy, achieving a good agreement with experimental data. In this work, we attempted to describe the unbinding process through WT-Metad simulations of the drug Danusertib, a potent type I inhibitor of Aurora a and B kinases, that presents similar Kd(M) of 1,69x10−9 for a and 1,44x10−9 for B. However, RT value for Danusertib is higher for Aurora B than for A, without a clear molecular and energetic explanation so far. We performed several replicates with WT-Metad of the drug unbinding in both complexed systems. Several conformations of Danusertib along the exit pathway from the active site were found and described. Additionally, we highlight key amino acids that can contribute to the drug's unbinding and the differential values of RT for Aurora a and B. Tentative unbinding paths, transition states along the exit routes were also estimated, allowing us to calculate the free binding energy (ΔG) of the process and therefore to estimate RT.