title: Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations.
abstract: Time-dependent inhibition of the cyclooxygenases (COX) by a range of nonsteroidal anti-inflammatory drugs has been described since the first experimental assays of COX were performed. Slow tight-binding inhibitors of COX-1 bind in a two-step mechanism in which the EI → EI* transition is slow and practically irreversible. Since then, various properties of the inhibitors have been proposed to cause or affect the time dependency. Conformational changes in the enzyme have also been proposed to cause the time dependency, but no particular structural feature has been identified. Here, we investigated a series of inhibitors of COX-1 that are either time-independent or time-dependent using a combination of molecular dynamics simulations, binding free energy calculations, and potential of mean force calculations. We find that the time-dependent inhibitors stabilize a conformational change in the enzyme mainly identified by the rotation of a leucine side chain adjacent to the binding pocket. The induced conformation has been previously shown to be essential for the high binding affinities of tight-binding inhibitors in COX-1. The results of this work show that the structural features of the enzyme involved in both time-dependent and tight-binding inhibition are identical and further identify a structural mechanism responsible for the transition between the two enzyme-inhibitor complexes characteristic of slow tight-binding COX-1 inhibitors.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , BMC, Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: Yasmin
authors.initials: Y
authors.lastname: Shamsudin
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , BMC, Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: Hugo
authors.initials: H
authors.lastname: Gutiérrez-de-Terán
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , BMC, Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: Johan
authors.identifier: 0000-0003-2091-0610
authors.initials: J
authors.lastname: Åqvist
mesh_terms: D000818:Animals; D000894:Anti-Inflammatory Agents, Non-Steroidal / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D051545:Cyclooxygenase 1 / Q000737:chemistry* / Q000378:metabolism; D016861:Cyclooxygenase Inhibitors / Q000737:chemistry*; D006801:Humans; D007052:Ibuprofen / Q000031:analogs & derivatives / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D012756:Sheep; D013045:Species Specificity; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D000894:Anti-Inflammatory Agents, Non-Steroidal; D016861:Cyclooxygenase Inhibitors; D051545:Cyclooxygenase 1; D007052:Ibuprofen