title: Assessing protein-ligand docking for the binding of organometallic compounds to proteins.
abstract: 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.
authors.affiliation: Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Ortega-Carrasco
authors.forename: Agusti
authors.initials: A
authors.lastname: Lledós
authors.forename: Jean-Didier
authors.initials: JD
authors.lastname: Maréchal
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D017076:Computer-Aided Design; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry*; D006801:Humans; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D009942:Organometallic Compounds / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D011494:Protein Kinases / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry*
chemical_list: D004791:Enzyme Inhibitors; D008024:Ligands; D009942:Organometallic Compounds; D011494:Protein Kinases; D014357:Trypsin
keywords: computational bioinorganics; drug design; kinase inhibition; metalodrugs; protein-ligand dockings