KMI-358 and KMI-370, highly potent and small-sized BACE1 inhibitors containing phenylnorstatine Tooru Kimura, a Daisuke Shuto, a Soko Kasai, a Ping Liu, a Koushi Hidaka, a Takashi Hamada, a Yoshio Hayashi, a Chinatsu Hattori, b Masashi Asai, b Shinobu Kitazume, c Takaomi C. Saido, d Shoichi Ishiura b and Yoshiaki Kiso a, * a Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan b Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan c Glyco-chain Functions Laboratory, Supra-biomolecular System Group, Frontier Research System, RIKEN, Wako-shi, Saitama 351-0198, Japan d Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, Saitama 351–0198, Japan Received 1 December 2003; accepted 26 December 2003 Abstract—Recently, we reported a novel substrate-based octapeptide BACE1 inhibitor KMI-008 containing hydroxy- methylcarbonyl (HMC) isostere as a transition-state mimic. Using KMI-008 as a lead compound, a small-sized and highly potent BACE1 inhibitor KMI-370 (IC 50 =3.4 nM) was designed and synthesized. # 2004 Elsevier Ltd. All rights reserved. 1. Introduction Cerebral deposition of amyloid fibrils as senile plaques is a pathological hallmark of Alzheimer’s disease (AD). 1 The predominant constituents of amyloid fibrils are 40- and 42-residue amyloid b peptides (Ab). Ab is generated from proteolytic processing of a transmembrane protein, b-amyloid precursor protein (APP). 2,3 Two proteases, called b- and g-secretases, cleave APP to generate the Ab peptide. b-Secretase which forms the N-terminus of Ab has been identified as a novel membrane-bound aspartic protease, BACE1 (memapsin 2 or Asp-2). 4 7 BACE1 plays a critical role in the progression of AD since the cleavage of APP by b-secretase is the first step in Ab formation. Therefore, the development of BACE1 inhibitor is valuable for the elucidation of AD pathol- ogy. Several transition-state analogue BACE1 inhibitors modelled on the b-secretase cleavage site have been reported with relatively low IC 50 values. 8 10 However, the molecular sizes of these inhibitors are too large to be viable drug candidates. On the basis of knowledge of our HIV-1 protease inhibitor studies, 11,12 we recently reported an octapeptide BACE1 inhibitor 1 (KMI-008) containing an unnatural amino acid, phenylnorstatine [(2R,3S)-3-amino-2-hydroxy-4- phenylbutyric acid: Pns], with a hydroxymethylcarbonyl (HMC) isostere as a transition-state mimic (Fig. 1). 13 KMI-008 showed potent inhibition against recombinant enzyme (IC 50 =413 nM) and decreased the secretion of sAPPb (a soluble form of APP generated by the action of b-secretase) from COS-7 cells co-transfected with both the APP and BACE1. However, the characteristics of KMI-008 were not suitable as a drug due to its large molecular weight, the presence of many natural peptide bonds, and no protection against exopeptidase. In this paper, we describe the design and synthesis of truncated BACE1 inhibitors which are more potent than KMI-008. 0960-894X/$ - see front matter # 2004 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2003.12.088 Bioorganic & Medicinal Chemistry Letters 14 (2004) 1527–1531 Figure 1. Structure of octapeptide BACE1 inhibitor, 1 (KMI-008). * Corresponding author. Tel.: +81-75-595-4635; fax: +81-75-591- 9900; e-mail: kiso@mb.kyoto-phu.ac.jp