Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel μM Leads for the Development of nM BACE-1 (β-Site APP Cleaving Enzyme 1) Inhibitors

Abstract

Fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design were used to identify novel inhibitors for BACE-1. A rapid optimization of an initial NMR hit was achieved by a combination of NMR and a functional assay, resulting in the identification of an isothiourea hit with a K(d) of 15 microM for BACE-1. NMR data and the crystal structure revealed that this hit makes H-bond interactions with the two catalytic aspartates, occupies the nonprime side region of the active site of BACE-1, and extends toward the S3 subpocket (S3sp). A focused NMR-based search for heterocyclic isothiourea isosteres resulted in several distinct classes of BACE-1 active site directed compounds with improved chemical stability and physicochemical properties. The strategy for optimization of the 2-aminopyridine lead series to potent inhibitors of BACE-1 was demonstrated. The structure-based design of a cyclic acylguanidine lead series and its optimization into nanomolar BACE-1 inhibitors are the subject of the companion paper

Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery

“…Nevertheless, fragment screening resulted in some early hits [73], which were followed up by successful FBDD campaigns [74, 75]. For example, Figure 3a shows a thioamidine core fragment identified by Schering-Plough researchers [76]. In contrast to the other targets we have discussed so far, in BACE-1 this fragment does not overlap well with CC1 ( FO =0.6), and hence conservation of the binding mode is not assured.…”

Advances in the identification of β-secretase inhibitors

“…Hit compound 84 (K d = 550 µM) and its improved form 85 (K d = 15 µM) were identified by fragment-based screening [139,140]. These hit compounds have an isothiourea moiety, and the X-ray crystal structure of 85--BACE1 complex revealed that the isothiourea moiety interacted with two Asp residues at the active site of BACE1.…”

BACE Inhibitors as Potential Drugs for the Treatment of Alzheimers Disease: Focus on Bioactivity

“…Stabilization of the thioisoureas by introducing heterocyclic structure provided iminohydanthoins with good drug properties and capable of inhibiting BACE1 at subnanomolar concentrations [106].…”