Accelerated Publications Subsite Specificity of Memapsin 2 (-Secretase): Implications for Inhibitor Design ² Robert T. Turner III, ‡,§ Gerald Koelsch, ‡,| Lin Hong, ‡,| Pedro Castanheira, ‡,⊥ Arun Ghosh, |,# and Jordan Tang* ,‡,§,| Protein Studies Program, Oklahoma Medical Research Foundation, and Department of Biochemistry and Molecular Biology, UniVersity of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, Zapaq, Inc., Oklahoma City, Oklahoma 73104, and Department of Chemistry, UniVersity of Illinois at Chicago, Chicago, Illinois 60607 ReceiVed May 30, 2001; ReVised Manuscript ReceiVed June 29, 2001 ABSTRACT: Memapsin 2 is the protease known as -secretase whose action on -amyloid precursor protein leads to the production of the -amyloid (A) peptide. Since the accumulation of A in the brain is a key event in the pathogenesis of Alzheimer’s disease, memapsin 2 is an important target for the design of inhibitory drugs. Here we describe the residue preference for the subsites of memapsin 2. The relative k cat /K M values of residues in each of the eight subsites were determined by the relative initial cleavage rates of substrate mixtures as quantified by MALDI-TOF mass spectrometry. We found that each subsite can accommodate multiple residues. The S 1 subsite is the most stringent, preferring residues in the order of Leu > Phe > Met > Tyr. The preferences of other subsites are the following: S 2 , Asp > Asn > Met; S 3 , Ile > Val > Leu; S 4 , Glu > Gln > Asp; S 1 ′, Met > Glu > Gln > Ala; S 2 ′, Val > Ile > Ala; S 3 ′, Leu > Trp > Ala; S 4 ′, Asp > Glu > Trp. In general, S subsites are more specific than the S′ subsites. A peptide comprising the eight most favored residues (Glu-Ile-Asp-Leu-Met-Val-Leu-Asp) was found to be hydrolyzed with the highest k cat /K M value so far observed for memapsin 2. Residue preferences at four subsites were also studied by binding of memapsin 2 to a combinatorial inhibitor library. From 10 tight binding inhibitors, the consensus preferences were as follows: S 2 , Asp and Glu; S 3 , Leu and Ile; S 2 ′, Val; and S 3 ′, Glu and Gln. An inhibitor, OM00-3, Glu-Leu-Asp-Leu*Ala-Val-Glu-Phe (where the asterisk represents the hydroxyethylene tansition-state isostere), designed from the consensus residues, was found to be the most potent inhibitor of memapsin 2 so far reported (K i of 3.1 × 10 -10 M). A molecular model of OM00-3 binding to memapsin 2 revealed critical improvement of the interactions between inhibitor side chains with enzyme over a previous inhibitor, OM99-2 [Ghosh, A. K., et al. (2000) J. Am. Chem. Soc. 14, 3522-3523]. The accumulation of -amyloid peptide (A) 1 in the brain is a major factor underlying the pathogenesis of Alzheimer’s disease (AD) (1). A is a fragment of a brain membrane protein -amyloid precursor protein (APP) produced by the activity of two proteases known as - and γ-secretases. -Secretase cleaves APP first in its lumenal domain and ² This work was partly supported by NIH Grant AG-18933. R.T.T. is a recipient of a Glenn/American Foundation for Aging Research Scholarship. G.K. is a Scientist Development Grant Awardee of the American Heart Association. J.T. is holder of the J. G. Puterbaugh Chair in Biomedical Research at the Oklahoma Medical Research Foundation. * To whom correspondence should be addressed at the Oklahoma Medical Research Foundation, 825 NE 13 St., Oklahoma City, OK 73104. Email: jordan-tang@omrf.ouhsc.edu. Tel: 405-271-7291. FAX: 405-271-7249. ‡ Oklahoma Medical Research Foundation. § University of Oklahoma Health Sciences Center. | Zapaq, Inc. ⊥ Present address: Department of Biochemistry, University of Coimbra, Coimbra, Portugal. # University of Illinois at Chicago. 1 Abbreviations: A, -amyloid peptide; APP, -amyloid precursor protein; AD, Alzheimer’s disease. © Copyright 2001 by the American Chemical Society Volume 40, Number 34 August 28, 2001 10.1021/bi015546s CCC: $20.00 © 2001 American Chemical Society Published on Web 08/03/2001