Apo and Inhibitor Complex Structures of BACE (β-secretase)

Human BACE, also known as β-secretase, shows promise as a potential therapeutic target for Alzheimer's disease. We determined the apo structure of BACE to 1.75 A, and a structure of a hydroxyethylamine inhibitor complex derived by soaking. These show significant active-site movements compared to previously described BACE structures. Additionally, the structures reveal two pockets that could be targeted by structure-based drug design.

[1]  J. Hardy,et al.  The Amyloid Hypothesis of Alzheimer ’ s Disease : Progress and Problems on the Road to Therapeutics , 2009 .

[2]  M. James,et al.  Crystal structure of human pepsin and its complex with pepstatin , 1995, Protein science : a publication of the Protein Society.

[3]  Tang,et al.  Proteolytic activation of recombinant pro-memapsin 2 (Pro-beta-secretase) studied with new fluorogenic substrates , 2000, Biochemistry.

[4]  C R Kissinger,et al.  Rapid automated molecular replacement by evolutionary search. , 1999, Acta crystallographica. Section D, Biological crystallography.

[5]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[6]  T L Blundell,et al.  X-ray analyses of aspartic proteinases. V. Structure and refinement at 2.0 A resolution of the aspartic proteinase from Mucor pusillus. , 1993, Journal of molecular biology.

[7]  A. Fedorov,et al.  Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution. , 1990, Journal of molecular biology.

[8]  J D Baxter,et al.  Structure of recombinant human renin, a target for cardiovascular-active drugs, at 2.5 A resolution. , 1989, Science.

[9]  L. Kuo,et al.  A general procedure for the purification of human beta-secretase expressed in Escherichia coli. , 2004, Protein expression and purification.

[10]  T L Blundell,et al.  X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution. , 1990, Journal of molecular biology.

[11]  L Hong,et al.  Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. , 2000, Science.

[12]  J. Wood,et al.  Structure-based drug design: the discovery of novel nonpeptide orally active inhibitors of human renin. , 2000, Chemistry & biology.

[13]  M. Takeuchi,et al.  Crystal structures of Aspergillus oryzae aspartic proteinase and its complex with an inhibitor pepstatin at 1.9A resolution. , 2003, Journal of molecular biology.

[14]  H. Cai,et al.  BACE1 is the major β-secretase for generation of Aβ peptides by neurons , 2001, Nature Neuroscience.

[15]  G. Cohen,et al.  Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis. , 1987, Journal of molecular biology.

[16]  J. Tang,et al.  Human aspartic protease memapsin 2 cleaves the beta-secretase site of beta-amyloid precursor protein. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[17]  R E Cachau,et al.  Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[18]  D. Rich,et al.  Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles. , 2002, Journal of medicinal chemistry.

[19]  A. Wlodawer,et al.  The three‐dimensional structure of recombinant bovine chymosin at 2.3 Å resolution , 1990, Proteins.

[20]  Alexander Wlodawer,et al.  An unusual orientation for Tyr75 in the active site of the aspartic proteinase from Saccharomyces cerevisiae. , 2002, Biochemical and biophysical research communications.

[21]  M. Ohno,et al.  BACE1 Deficiency Rescues Memory Deficits and Cholinergic Dysfunction in a Mouse Model of Alzheimer's Disease , 2004, Neuron.

[22]  B. de Strooper,et al.  Novel therapeutic strategies provide the real test for the amyloid hypothesis of Alzheimer's disease. , 2002, Trends in pharmacological sciences.

[23]  D S Moss,et al.  Main-chain bond lengths and bond angles in protein structures. , 1993, Journal of molecular biology.

[24]  J. Quail,et al.  Crystal structure of the aspartic proteinase from Rhizomucor miehei at 2.15 A resolution. , 1997, Journal of molecular biology.

[25]  Alice Stanton,et al.  Structure-based design of aliskiren, a novel orally effective renin inhibitor. , 2003, Biochemical and biophysical research communications.

[26]  R. Heinrikson,et al.  Human β-Secretase (BACE) and BACE Inhibitors , 2003 .

[27]  Tom Blundell,et al.  The active site of aspartic proteinases , 1991, FEBS letters.

[28]  S. Roggo.  Inhibition of BACE, a promising approach to Alzheimer's disease therapy. , 2002, Current topics in medicinal chemistry.

[29]  F. Winkler,et al.  Renin inhibition by substituted piperidines: a novel paradigm for the inhibition of monomeric aspartic proteinases? , 1999, Chemistry & biology.

[30]  W. Richards,et al.  Mice deficient in BACE1, the Alzheimer's β-secretase, have normal phenotype and abolished β-amyloid generation , 2001, Nature Neuroscience.

[31]  Lin Hong,et al.  Crystal Structure of Memapsin 2 (β-Secretase) in Complex with an Inhibitor OM00-3† , 2002 .

[32]  V S Lamzin,et al.  wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models. , 1997, Acta crystallographica. Section D, Biological crystallography.

[33]  T. Blundell,et al.  X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution. , 1990, Journal of molecular biology.

[34]  D. Timm,et al.  Phe*-Ala-based pentapeptide mimetics are BACE inhibitors: P2 and P3 SAR. , 2004, Bioorganic & medicinal chemistry letters.

[35]  Michael J. Hartshorn,et al.  AstexViewerTM †: a visualisation aid for structure-based drug design , 2002, J. Comput. Aided Mol. Des..

[36]  C. Oefner,et al.  Substituted piperidines--highly potent renin inhibitors due to induced fit adaptation of the active site. , 1999, Bioorganic & medicinal chemistry letters.

[37]  M. Kansy,et al.  Piperidine-renin inhibitors compounds with improved physicochemical properties. , 1999, Bioorganic & medicinal chemistry letters.

[38]  R. Barbour,et al.  Purification and cloning of amyloid precursor protein β-secretase from human brain , 1999, Nature.

[39]  H. Jhoti,et al.  Structure-based screening of low-affinity compounds. , 2002, Drug discovery today.

[40]  F. Diederich,et al.  Development of a New Class of Inhibitors for the Malarial Aspartic Protease Plasmepsin II Based on a Central 7‐Azabicyclo[2.2.1]heptane Scaffold , 2003 .

[41]  D. Banner,et al.  Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. , 1994, The Journal of biological chemistry.

[42]  Eugene D. Thorsett,et al.  Design and synthesis of statine-based cell-permeable peptidomimetic inhibitors of human beta-secretase. , 2003, Journal of medicinal chemistry.

[43]  D. Teplow,et al.  A Furin-like Convertase Mediates Propeptide Cleavage of BACE, the Alzheimer's β-Secretase* , 2000, The Journal of Biological Chemistry.

[44]  J. Yon,et al.  Recombinant insect cell expression and purification of human beta-secretase (BACE-1) for X-ray crystallography. , 2002, Protein expression and purification.

[45]  Lin Hong,et al.  Flap position of free memapsin 2 (beta-secretase), a model for flap opening in aspartic protease catalysis. , 2004, Biochemistry.

[46]  J. Treanor,et al.  Beta-secretase cleavage of Alzheimer's amyloid precursor protein by the transmembrane aspartic protease BACE. , 1999, Science.

[47]  S. Cho,et al.  Structure of aspergillopepsin I from Aspergillus phoenicis: variations of the S1'-S2 subsite in aspartic proteinases. , 2001, Acta crystallographica. Section D, Biological crystallography.

[48]  David G. Tew,et al.  Identification of a Novel Aspartic Protease (Asp 2) as β-Secretase , 1999, Molecular and Cellular Neuroscience.

[49]  M. James,et al.  Structure and refinement of penicillopepsin at 1.8 A resolution. , 1983, Journal of molecular biology.

[50]  T. L. Blundell,et al.  X-ray analyses of peptide–inhibitor complexes define the structural basis of specificity for human and mouse renins , 1992, Nature.