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ACS Med Chem Lett. 2011 Aug 27;2(11):834-9. doi: 10.1021/ml2001505. eCollection 2011 Nov 10.

Homology Model and Docking-Based Virtual Screening for Ligands of the σ1 Receptor.

Author information

1
Molecular Simulation Engineering (MOSE) Laboratory, Department of Industrial Engineering and Information Technology (DI3), University of Trieste , Via Valerio 10, 34127 Trieste, Italy.
2
Department of Pharmaceutical Sciences, University of Trieste , Piazzale Europa 1, 34127 Trieste, Italy.

Abstract

This study presents for the first time the 3D model of the σ1 receptor protein as obtained from homology modeling techniques, shows the applicability of this structure to docking-based virtual screening, defines a computational strategy to optimize the results based on a combination of 3D pharmacophore-based docking and MM/PBSA free energy of binding scoring, and provides evidence that these in silico models and recipes are powerful tools on which virtual screening of new σ1 ligands can be based. In particular, the validation of the applicability of docking-based virtual screening to homology models is of utmost importance, since no crystal structure is available to date for the σ1 receptor, and this missing information still constitutes a major hurdle for a rational ligand design for this important protein target.

KEYWORDS:

3D pharmacophore model; docking; free energy of binding; homology modeling; virtual screening; σ1 Receptor

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