Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations

In silico virtual screening (VS) is a powerful hit identification technique used in drug discovery projects that aims to effectively distinguish true actives from inactive or decoy molecules. To better capture the dynamic behavior of protein drug targets, compound databases may be screened against an ensemble of protein conformations, which may be experimentally determined or generated computationally, i.e. via molecular dynamics (MD) simulations. Several studies have shown that conformations generated by MD are useful in identifying novel hit compounds, in part because structural rearrangements sampled during MD can provide novel targetable areas. However, it remains difficult to predict a priori when an MD conformation will outperform a VS against the crystal structure alone. Here, we assess whether MD conformations result in improved VS performance for six protein kinases. MD conformations are selected using three different methods, and their VS performances are compared to the corresponding crystal structures. Additionally, these conformations are used to train ensembles, and their VS performance is compared to the individual MD conformations and the corresponding crystal structures using receiver operating characteristic curve (ROC) metrics. We show that performing MD results in at least one conformation that offers better VS performance than the crystal structure, and that, while it is possible to train ensembles to outperform the crystal structure alone, the extent of this enhancement is target dependent. Lastly, we show that the optimal structural selection method is also target dependent and recommend optimizing virtual screens on a kinase-by-kinase basis to improve the likelihood of success.