A Molecular Dynamics–Shared Pharmacophore Approach to Boost Early‐Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator‐Activated Receptor α. (17th February 2017)

• Record Type: Journal Article
• Authors: Perricone, Ugo; Wieder, Marcus; Seidel, Thomas; Langer, Thierry; Padova, Alessandro; Almerico, Anna Maria; Tutone, Marco
• Is Part Of: ChemMedChem. Volume 12:Number 16(2017)
• Page Start: 1399
• Page End: 1407
• Publication Date: 2017-02-17
• Subjects: drug design -- dynamic pharmacophores -- molecular docking -- PPARα -- virtual screening; Pharmaceutical chemistry -- Periodicals; 615.19005
• DOI: 10.1002/cmdc.201600526
• Languages: English
• ISSNs: 1860-7179

Abstract

Abstract: Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co‐crystallized ligands can help elucidate the role of the ligand on a protein′s active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand–protein interactions within the complexes. The study was carried out on peroxisome proliferator‐activated receptor α (PPARα). Findings derived from the dynamic analysis of interactions were then used as features for pharmacophore generation and constraints for generating the docking grid for use in virtual screening. We found that information derived from short multiple MD simulations using different molecules within the binding pocket of the target can improve the early enrichment of active ligands in the virtual screening process for this receptor. In the end we adopted a consensus scoring based on docking score and pharmacophore alignment to rank our dataset. Our results showed an improvement in virtual screening performance in early recognition when screening was performed with the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach. Abstract : The MYSHAPE approach is a new way of studying ligand–receptor interactions. In this method, a pharmacophore model is created that exploits information derived from multiple short MD simulations, using different molecules within the binding pocket of the target. Conformational information is retrieved from the full trajectory and not only from clustered frames. This approach can help improve virtual screening performance, especially for the early enrichment of active ligands in the virtual screening process.