title: Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.
abstract: We have developed a method to dock a transition-state structure into the active site of an enzyme. Such an approach is more discriminative than standard docking when looking for substrates of an enzyme, because a transition state has more sterical restrictions than a nonreactive state. We use an accurate and tailored force field for the transition-state for the hydroxylation reaction in cytochrome P450, obtained with the Q2MM method. We apply this method to the docking of two drugs, progesterone and flunitrazepam, to the active sites of two human cytochromes P450, 2C9 and 3A4. We obtain a qualitative agreement compared to experiments, both for hydrogen atoms bound to the same carbon atom (for which the force-field energies are directly comparable) and for general sites on the drug molecules, if the method is combined with an estimate of the intrinsic reactivity of the various sites. However, the method does not rank all the sites correctly. It is not significantly improved if the proteins are allowed to relax locally or if it is combined with the MM/PBSA approach, which fully accounts for the protein flexibility and explicitly treats solvation and entropy effects. On the other hand our method performs better than standard docking with the GOLD software or predictions of metabolic sites with the MetaSite software.
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Patrik
authors.initials: P
authors.lastname: Rydberg
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Sine Myrup
authors.initials: SM
authors.lastname: Hansen
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Jacob
authors.initials: J
authors.lastname: Kongsted
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Per-Ola
authors.initials: PO
authors.lastname: Norrby
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Lars
authors.initials: L
authors.lastname: Olsen
authors.affiliation: Biostructural Research Group, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark, Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden, and Department of Chemistry, University of Gothenburg, Kemigården 4, SE-412 96 Göteborg, Sweden.
authors.forename: Ulf
authors.initials: U
authors.lastname: Ryde