Application of Free Energy Perturbation for the Design of BACE1 Inhibitors

作者：Ciordia Myriam; Perez Benito Laura; Delgado Francisca; Trabanco Andres A^*; Tresadern Gary^*

来源：Journal of Chemical Information and Modeling, 2016, 56(9): 1856-1871.

DOI：10.1021/acs.jcim.6b00220

Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of beta-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting molecules showed pIC(50) potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the Calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.

• 出版日期2016-9