title: Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1.
abstract: Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used for the treatment of pain, fever, inflammation, and some types of cancers. Their mechanism of action is the inhibition of isoforms 1 and 2 of the enzyme cyclooxygenase (COX-1 and COX-2, respectively). However, both nonselective and selective NSAIDs may have side effects that include gastric intestinal bleeding, peptic ulcer formation, kidney problems, and occurrences of myocardial infarction. The search for selective high-affinity COX inhibitors resulted in a number of compounds characterized by a slow, tight-binding inhibition that occurs in a two-step manner. It has been suggested that the final, only very slowly reversible, tight-binding event is the result of conformational changes in the enzyme. However, the nature of these conformational changes has remained elusive. Here we explore the structural determinants of the tight-binding phenomenon in COX-1 with molecular dynamics and free energy simulations. The calculations reveal how different classes of inhibitors affect the equilibrium between two conformational substates of the enzyme in distinctly different ways. The class of tight-binding inhibitors is found to exclusively stabilize an otherwise unfavorable enzyme conformation and bind significantly stronger to this state than to that normally observed in crystal structures. By also computing free energies of binding to the two enzyme conformations for 16 different NSAIDs, we identify an induced-fit mechanism and the key structural features associated with high-affinity tight binding. These results may facilitate the rational development of new COX inhibitors with improved selectivity profiles.
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden.
authors.forename: Yasmin
authors.initials: Y
authors.lastname: Shamsudin
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, SE-751 24 Uppsala, Sweden.
authors.forename: Masoud
authors.initials: M
authors.lastname: Kazemi
authors.affiliation: Department of Cell and Molecular Biology, Uppsala University , Box 596, BMC, 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 , Box 596, BMC, SE-751 24 Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Åqvist
mesh_terms: D018360:Crystallography, X-Ray; D051545:Cyclooxygenase 1 / Q000737:chemistry*; D051546:Cyclooxygenase 2 / Q000737:chemistry; D016861:Cyclooxygenase Inhibitors / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding
chemical_list: D016861:Cyclooxygenase Inhibitors; D051545:Cyclooxygenase 1; D051546:Cyclooxygenase 2; C496511:PTGS1 protein, human; C496540:PTGS2 protein, human