title: Effect of the protonation state of the titratable residues on the inhibitor affinity to BACE-1.
abstract: BACE-1 is one of the aspartic proteases involved in the cleavage of beta amyloid peptide, an initial step in the formation of amyloid plaques whose toxicity induces neuron death in Alzheimer's disease patients. One of the central issues in the search of novel BACE-1 inhibitors is the optimum pH for the binding of inhibitors to the enzyme. It is known that the enzyme has optimal catalytic activity at acidic pH, while cell active inhibitors may bind optimally at higher pH. In this work we determine the effect of the pH on the affinities of a set of inhibitors, with a variety of chemical motifs, for the ectodomain region of BACE-1 by a surface plasmon resonance (SPR) biosensor based assay. In order to understand the molecular interactions that underlie the diverse optimum pH for the binding of the various inhibitors as observed experimentally, we have calculated the titration curves for a set of BACE-1 ligand complexes. The results indicate that the pK(a) values of the titratable residues of the protein depend on the nature of the ligand involved, in disagreement with previous work. The enzyme-inhibitor structures with the resulting protonation states at pH values 4.5 and 7.4 served as the starting point for the prediction of the pH-dependent binding ranking. Our calculations reproduced the entire affinity ranking observed upon pH increase and most of the binding trends among inhibitors, especially at low pH. Finally, our cell-based assays indicate a possible correlation between high inhibitor affinity at both acidic and neutral pH values, with optimal cell response, a result that may open new venues for the search of potent BACE-1 inhibitors that are active at the cellular level.
authors.affiliation: Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors.forename: José L
authors.initials: JL
authors.lastname: Domínguez
authors.forename: Tony
authors.initials: T
authors.lastname: Christopeit
authors.forename: M Carmen
authors.initials: MC
authors.lastname: Villaverde
authors.forename: Thomas
authors.initials: T
authors.lastname: Gossas
authors.forename: José M
authors.initials: JM
authors.lastname: Otero
authors.forename: Susanne
authors.initials: S
authors.lastname: Nyström
authors.forename: Vera
authors.initials: V
authors.lastname: Baraznenok
authors.forename: Erik
authors.initials: E
authors.lastname: Lindström
authors.forename: U Helena
authors.initials: UH
authors.lastname: Danielson
authors.forename: Fredy
authors.initials: F
authors.lastname: Sussman
mesh_terms: D016564:Amyloid beta-Protein Precursor; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D006801:Humans; D008024:Ligands; D055585:Physical Phenomena; D058255:Protease Nexins; D017434:Protein Structure, Tertiary; D011956:Receptors, Cell Surface
chemical_list: D016564:Amyloid beta-Protein Precursor; D004791:Enzyme Inhibitors; D008024:Ligands; D058255:Protease Nexins; D011956:Receptors, Cell Surface