Docking to heme proteins

In silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron–ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme‐containing complexes with iron‐ligand contact. By introducing Morse‐like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand–water interactions in the X‐ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross‐docking studies. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009