Discovery of a Novel Warhead against β-Secretase through Fragment-Based Lead Generation

Abstract

Fragment-based lead generation was applied to find novel small-molecule inhibitors of beta-secretase (BACE-1), a key target for the treatment of Alzheimer's disease. Fragment hits coming from a 1D NMR screen were characterized by BIAcore, and the most promising compounds were soaked into protein crystals to help the rational design of more potent hit analogues. Problems arising due to our inability to grow BACE-1 crystals at the biologically relevant pH at which the screen was run were overcome by using endothiapepsin as a surrogate aspartyl protease. Among others, we identified 6-substituted isocytosines as a novel warhead against BACE-1, and the accompanying paper in this journal describes how these were optimized to a lead series of nanomolar inhibitors.1.

Structure and modeling in the design of β‐ and γ‐secretase inhibitors

“…Several examples are shown in Figure 10. These can be roughly classified by their transition state mimic and include: (1) peptidomimetic designs incorporating statine Hu et al, 2003Hu et al, , 2004Lamar et al, 2004;Tung et al, 2002], hydroxymethylcarbonyl [Hamada et al, 2006[Hamada et al, , 2008aShuto et al, 2003], or hydroxyethylene [Brady et al, 2004;Ghosh et al, 2006;Hanessian et al, 2005;Hom et al, 2004;Xiao et al, 2006]; (2) nonpeptidic designs incorporating a reduced amide , hydroxymethylcarbonyl [Hamada et al, 2008a,b] hydroxyethylene [Ghosh et al, 2007], hydroxyethylamine Freskos et al, 2007a,b;Ghosh et al, 2008;Kortum et al, 2007;Maillard et al, 2007;Park et al, 2008;Stachel et al, 2004Stachel et al, , 2006Stauffer et al, 2007], aminoethylene , or tertiary carbinamine [Lindsley et al, 2007;Rajapakse et al, 2006]; (3) arylpiperazines [Garino et al, 2006]; (4) acylguanidines Fobare et al, 2007;Jennings et al, 2008]; (5) dihydroquinazolines [Baxter et al, 2007]; (6) isocytosines Geschwindner et al, 2007]; (7) pyrrolidine/piperidines [Iserloh et al,Fig. 9.…”

“…Recently, true fragment-based screens have been reported by groups at Astex [Murray et al, 2007], AstraZeneca Geschwindner et al, 2007], and Hoffmann-La Roche [Kuglstatter et al, 2008]. In the Astex screen [Murray et al, 2007], an initial set of 347 ''drug-like'' fragments (MWo300, cLogPo3, and H-bond donorso4) was soaked into the BACE-1 active site in cocktails of six.…”

Library screening by fragment‐based docking

“…Thus the importance of molecular fragments has been recognized and exploited first by computational approaches. 1,3,4 More recently, fragment-based drug discovery strategies have been developed using X-ray crystallography, 5 nuclear magnetic resonance spectroscopy, 6 surface plasmon resonance, 7 mass spectrometry, 8,9 substrate activity screening (where the fragments are substrates later converted into inhibitors [10][11][12] ), and tethering. 13,14 Experimental techniques for fragment-based drug discovery have been discussed in previous reviews which contain a large number of applications.…”

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry

“…This class of enzymes play a causative role in important diseases such as malaria, Alzheimer's disease, hypertension, and AIDS 23. Owing to its high similarity with these drug targets, endothiapepsin has been used as a model enzyme for mechanistic studies24, 25, 26 and for the discovery of inhibitors of renin27 and β‐secretase 28. Endothiapepsin is a robust enzyme, which remains active for more than 20 days at room temperature, is readily available in large quantities, and crystallizes easily, thus making it a useful representative for aspartic proteases 18.…”