title: Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.
abstract: Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein-ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low-energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol-O-methyltransferase and BIA 9-1067, a newly developed tight-binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high-binding affinity (K(d) in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O-methylated product. By comparing the experimental catalytic rate (k(cat)) and the estimated dissociation rate (k(off)) constants of the enzyme-inhibitor complex, one can conclude that the observed inhibition potency (K(i)) is primarily dependent on the catalytic rate constant of the inhibitor's O-methylation, rather than the rate constant of dissociation of the complex.
authors.affiliation: BIAL, Department of Research and Development, S Mamede do Coronado, Portugal. nuno.palma@bial.com
authors.forename: P Nuno
authors.initials: PN
authors.lastname: Palma
authors.forename: Maria João
authors.initials: MJ
authors.lastname: Bonifácio
authors.forename: Ana Isabel
authors.initials: AI
authors.lastname: Loureiro
authors.forename: Patrício
authors.initials: P
authors.lastname: Soares-da-Silva
mesh_terms: D002394:Catechol O-Methyltransferase / Q000378:metabolism*; D065098:Catechol O-Methyltransferase Inhibitors; D003198:Computer Simulation; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D010069:Oxadiazoles / Q000737:chemistry / Q000494:pharmacology*; D010300:Parkinson Disease / Q000188:drug therapy / Q000201:enzymology; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D065098:Catechol O-Methyltransferase Inhibitors; D004791:Enzyme Inhibitors; D010069:Oxadiazoles; D002394:Catechol O-Methyltransferase; C549349:opicapone