Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors

Abstract

The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer’s disease. However, the development of clinically useful BACE-1 inhibitors has proven to be extremely challenging. In this study we examine the binding mode of a novel potent inhibitor (compound 1, with IC50 80 nM) designed by synergistic combination of two fragments—huprine and rhein—that individually are endowed with very low activity against BACE-1. Examination of crystal structures reveals no appropriate binding site large enough to accommodate 1. Therefore we have examined the conformational flexibility of BACE-1 through extended molecular dynamics simulations, paying attention to the highly flexible region shaped by loops 8–14, 154–169 and 307–318. The analysis of the protein dynamics, together with studies of pocket druggability, has allowed us to detect the transient formation of a secondary binding site, which contains Arg307 as a key residue for the interaction with small molecules, at the edge of the catalytic cleft. The formation of this druggable “floppy” pocket would enable the binding of multisite inhibitors targeting both catalytic and secondary sites. Molecular dynamics simulations of BACE-1 bound to huprine-rhein hybrid compounds support the feasibility of this hypothesis. The results provide a basis to explain the high inhibitory potency of the two enantiomeric forms of 1, together with the large dependence on the length of the oligomethylenic linker. Furthermore, the multisite hypothesis has allowed us to rationalize the inhibitory potency of a series of tacrine-chromene hybrid compounds, specifically regarding the apparent lack of sensitivity of the inhibition constant to the chemical modifications introduced in the chromene unit. Overall, these findings pave the way for the exploration of novel functionalities in the design of optimized BACE-1 multisite inhibitors.

Spatiotemporal identification of druggable binding sites using deep learning

“…Proteins are flexible molecules, that adopt various conformations during their life cycle; and a binding site is a dynamic property of a protein mediated by its conformational changes 6 , 7 . Single protein structure represents only a minor part of the entire conformational space, hence, binding sites might be easy to overlook from the experimentally determined three-dimensional protein structures 8 , 9 . Moreover, many proteins perform their function assembling to oligomeric structure and can form binding sites by means of oligomer’s subunits 10 , 11 .…”

Spatiotemporal identification of druggable binding sites using deep learning

“…Proteins are flexible molecules, that adopt various conformations during their life cycle; and a binding site is a dynamic property of a protein mediated by its conformational changes [6,7]. Single protein structure represents only minor part of the entire conformational ensemble, hence, binding sites might be easy to overlook from the experimentally determined three-dimensional protein structures [8,9]. Moreover, many proteins perform their function assembling to oligomeric structure and can form binding sites by means of oligomer's subunits [10,11].…”

pH‐dependent conformational dynamics of beta‐secretase 1: A molecular dynamics study

“…By accounting explicitly for the possibility of multiple protonation states, we can vastly improve our understanding of pH‐dependent conformational changes and the associated changes in electrostatic environment. Previous studies have attempted to use constant pH or other forms of MD to study BACE‐1 dynamics. To our knowledge, this is the first study to use explicit solvent CpH‐MD to quantitatively examine the effect of pH on water lifetimes in BACE‐1 and to attempt to correlate this with a conformational change in the protein towards the understanding of the source of the pH dependence of BACE‐1 activity.…”