Assessing protein–ligand docking for the binding of organometallic compounds to proteins
Article first published online: 28 OCT 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 35, Issue 3, pages 192–198, 30 January 2014
How to Cite
How to cite this article: J. Comput. Chem. 2014, 35, 192–198. DOI: 10.1002/jcc.23472., , .
- Issue published online: 25 DEC 2013
- Article first published online: 28 OCT 2013
- Manuscript Accepted: 29 SEP 2013
- Manuscript Revised: 25 SEP 2013
- Manuscript Received: 21 JUN 2013
- Ministerio de Economía y Competitividad. Grant Number: CTQ2011-23336
- ORFEO Consolider-Ingenio 2010 Programme. Grant Number: CSD2007-00006
- Generalitat de Catalunya. Grant Number: 2009SGR68
- Universitat Autònoma de Barcelona (E. Ortega-Carrasco)
- protein–ligand dockings;
- computational bioinorganics;
- kinase inhibition;
- drug design
Organometallic compounds are increasingly used as molecular scaffolds in drug development projects; their structural and electronic properties offering novel opportunities in protein–ligand complementarities. Interestingly, while protein–ligand dockings have long become a spearhead in computer assisted drug design, no benchmarking nor optimization have been done for their use with organometallic compounds. Pursuing our efforts to model metal mediated recognition processes, we herein present a systematic study of the capabilities of the program GOLD to predict the interactions of protein with organometallic compounds. The study focuses on inert systems for which no alteration of the first coordination sphere of the metal occurs upon binding. Several scaffolds are used as test systems with different docking schemes and scoring functions. We conclude that ChemScore is the most robust scoring function with ASP and ChemPLP providing with good results too and GoldScore slightly underperforming. This study shows that current state-of-the-art protein-ligand docking techniques are reliable for the docking of inert organometallic compounds binding to protein. © 2013 Wiley Periodicals, Inc.