A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor α

Marco Tutone, Ugo Perricone, Anna Maria Almerico, Ugo Perricone, Marcus Wieder, Thomas Seidel, Alessandro Padova, Thierry Langer

Risultato della ricerca: Articlepeer review

19 Citazioni (Scopus)

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 receptorα (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.
Lingua originaleEnglish
pagine (da-a)1399-1407
Numero di pagine9
RivistaChemMedChem
Volume12
Stato di pubblicazionePublished - 2017

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Pharmacology
  • Drug Discovery
  • Molecular Medicine
  • ???subjectarea.asjc.3000.3000???
  • Organic Chemistry

Fingerprint Entra nei temi di ricerca di 'A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor α'. Insieme formano una fingerprint unica.

Cita questo