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

Di Pietro, Ornella; Juarez-Jimenez, Jordi; Munoz-Torrero, Diego; Laughton, Charles A.; Luque, F. Javier

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 challeng- ing. 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 bind- ing 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 oligo- methylenic 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 intro- duced 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.

Citation

Di Pietro, O., Juarez-Jimenez, J., Munoz-Torrero, D., Laughton, C. A., & Luque, F. J. (2017). Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: conformational analysis and binding mode of multisite inhibitors. PLoS ONE, 12(5), Article e0177683. https://doi.org/10.1371/journal.pone.0177683

• Journal Article Type: Article
• Acceptance Date: May 1, 2017
• Publication Date: May 15, 2017
• Deposit Date: May 19, 2017
• Publicly Available Date: May 19, 2017
• Journal: PLoS ONE
• Electronic ISSN: 1932-6203
• Publisher: Public Library of Science
• Peer Reviewed: Peer Reviewed
• Volume: 12
• Issue: 5
• Article Number: e0177683
• DOI: https://doi.org/10.1371/journal.pone.0177683
• Public URL: https://nottingham-repository.worktribe.com/output/860706
• Publisher URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0177683
• Contract Date: May 19, 2017