Nuclear hormone receptor targeted virtual screening.

Virtual library screening (VLS) is emerging as a valuable drug lead discovery tool. ICM-VLS implementation of this technology was evaluated on a benchmark set of nuclear hormone receptors (NRs), an important therapeutic target family. Over 5000 structurally diverse compounds, including 78 known NR ligands, were screened against 18 crystal structures and one computer model of 10 NR ligand binding domains in their active or inactive states. The results confirm the ability of the VLS method to generate highly focused subsets of the input chemical library, enriched 33- to 100-fold for all but one receptor studied. However, receptor flexibility remains to be fully addressed, and the choice of the specific conformation used for screening may determine the success of the exercise. We observe that for a particular ligand VLS can often identify the correct target within the receptor family, although the technology is unable to reliably discriminate between the closely related receptor isoforms. Additionally, our results suggest that VLS may be applied successfully without an experimental structure of the receptor by using a homology model. These data represent a realistic snapshot of the state-of-the-art of NR-targeted VLS and define the recent progress and the remaining limitations of the technology.