Structure-guided design of β-secretase (BACE-1) inhibitors

Bibliography

• CITRON M: Strategies for disease modification in Alzheimer's disease. Nat. Rev. Neurosci. (2004) 5:677-685.
   PubMed Web of Science ®Google Scholar
• BEHER D, GRAHAM SL: Protease inhibitors as potential disease-modifying therapeutics for Alzheimer's disease. Expert Opin. Investig. Drugs (2005) 14:1385-1409.
   PubMed Web of Science ®Google Scholar
• POSTINA R, SCHROEDER A, DEWACHTER I et al.: A disintegrin-metalloproteinase prevents amyloid plaque formation and hippocampal defects in an Alzheimer disease mouse model. J. Clin. Invest. (2004) 113:1456-1464.
   PubMed Web of Science ®Google Scholar
• HONG L, KOELSCH G, LIN X et al.: Structure of the protease domain of memapsin 2 (β-secretase) complexed with inhibitor. Science (2000) 290:150-153.
   PubMed Web of Science ®Google Scholar
• PATEL S, VUILLARD L, CLEASBY A et al.: Apo and inhibitor complex structures of BACE (β-secretase). J. Mol. Biol. (2004) 343:407-416.
   PubMed Web of Science ®Google Scholar
• COBURN CA, STACHEL SJ, LI Y-M et al.: Identification of a small molecule nonpeptide active site β-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases. J. Med. Chem. (2004) 47:6117-6119.
   PubMed Web of Science ®Google Scholar
• ANNIS DA, ATHANASOPOULOS J, CURRAN P et al.: An affinity selection-mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries. Discovery of a novel antagonist of E. coli dihydrofolate reductase. Intern. J. Mass. Spect. (2004) 238(2):77-83.
   Web of Science ®Google Scholar
• KORNACKER MG, LAI Z, WITMER K et al.: An inhibitor binding pocket distinct from the catalytic active site on human β-APP cleaving enzyme. Biochemistry (2005) 44:11567-11573.
   PubMed Web of Science ®Google Scholar
• STACHEL SJ, COBURN CA, STEELE TG et al.: Conformationally biased P3 amide replacements of β-secretase inhibitors. Bioorg. Med. Chem. Lett. (2006) 16:641-644.
   PubMed Web of Science ®Google Scholar
• RAJAPAKSE HA, NANTERMET PG, SELNICK HG et al.: Discovery of oxadiazole tertiary carbinamine inhibitors of β-secretase (BACE-1). J. Med. Chem. (2006) 49:7270-7273.
   PubMed Web of Science ®Google Scholar
• RAJAMANI R, REYNOLDS CH: Modeling the protonation states of the catalytic aspartates in β-secretase. J. Med. Chem. (2004) 47(21):5159-5166.
   PubMed Web of Science ®Google Scholar
• WANG Y-X, FREEDBERG DI, YAMAZAKI T et al.: Solution NMR evidence that the HIV-1 protease catalytic aspartyl groups have different ionization states in the complex formed with the asymmetric drug KNI-272. Biochemistry (1996) 35:9945-9950.
   PubMed Web of Science ®Google Scholar
• YU N, HAYIK SA, WANG B et al.: Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement. J. Chem. Theory Comp. (2006) 2(4):1057-1069.
   PubMed Web of Science ®Google Scholar
• PARK H, LEE S: Determination of the active site protonation state of β-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. J. Am. Chem. Soc. (2003) 125(52):16416-16422.
   PubMed Web of Science ®Google Scholar
• POLGAR T, KESERU GM: Virtual screening for β-secretase ( BACE1 ) inhibitors reveals the importance of protonation states at Asp32 and Asp228. J. Med. Chem. (2005) 48(11):3749-3755.
   PubMed Web of Science ®Google Scholar
• POLGAR T, KESERU GM: Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and β-secretase. J. Chem. Inf. Model (2006) 46:1795-1805.
   PubMed Web of Science ®Google Scholar
• HONG L, TANG J: Flap position of free memapsin 2 (β-secretase), a model for flap opening in aspartic protease catalysis. Biochemistry (2004) 43:4689-4695.
   PubMed Web of Science ®Google Scholar
• RENNER S, SCHNEIDER G: Scaffold-hopping potential of ligand-based similarity concepts. Chem. Med. Chem. (2006) 1:181-185.
   Google Scholar
• FECHNER U, FRANKE L, RENNER S et al.: Comparison of correlation vector methods for ligand-based similarity searching. J. Comp. Aid. Mol. Des. (2003) 17:687-698.
   PubMed Web of Science ®Google Scholar
• MCGAUGHEY GB, SHERIDAN RP, BAYLY CI et al.: Comparison of topological, shape, and docking methods in virtual screening. JCIM (2007) asap.
   Google Scholar
• MURRAY C, CALLAGHAN O, CHESSARI G et al.: Application of fragment screening by X-ray crystallography to β-secretase. J. Med. Chem. (2007) 50:1116-1123.
   PubMed Web of Science ®Google Scholar
• COLE DC, MANAS ES, STOCK JR et al.: Acylguanidines as small-molecule β-secretase inhibitors. J. Med. Chem. (2006) 49:6158-6161.
   PubMed Web of Science ®Google Scholar
• JONES G, WILLETT P, GLEN RC et al.: Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. (1995) 245:43-53.
   PubMed Web of Science ®Google Scholar
• JONES G, WILLETT P, GLEN R et al.: Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. (1997) 267:727-748.
   PubMed Web of Science ®Google Scholar
• ELDRIDGE MD, MURRAY CW, AUTON TR et al.: Empirical scoring functions 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comp. Aid. Mol. Des. (1997) 11:425-445.
   PubMed Web of Science ®Google Scholar
• VERDONK ML, COLE, JC, HARTSHORN M et al.: Improved protein-ligand docking using GOLD. Proteins (2003) 52:609-623.
   PubMed Web of Science ®Google Scholar
• DURHAM TB, SHEPHERD TA: Progress toward the discovery and development of efficacious BACE inhibitors. Curr. Opin. Drug Discov. Develop. (2006) 9:776-791.
   PubMed Web of Science ®Google Scholar
• TOUNGE BA, REYNOLDS CH: Calculation of the binding affinity of β-secretase inhibitors using the linear interaction energy method. J. Med. Chem. (2003) 46:2074-2082.
   PubMed Web of Science ®Google Scholar
• TOUNGE BA, RAJAMANI R, BAXTER EW et al.: Linear interaction energy models for β-secretase (BACE) inhibitors: role of van der Waals, electrostatic, and continuum-solvation terms. J. Mol. Graph. Model (2006) 24:475-484.
   PubMed Web of Science ®Google Scholar
• AQVIST J, MARELIUS J: The linear interaction energy method for predicting ligand binding free energies. Comb. Chem. High Throughput Screen. (2001) 4:613-626.
   PubMed Web of Science ®Google Scholar
• GHOSH AK, BOLCER G, HARWOOD C et al.: Structure-based design: potent inhibitors of human brain memapsin 2 (β-secretase). J. Med. Chem. (2001) 44:2865.
   PubMed Web of Science ®Google Scholar
• GHOSH AK, SHIN D, DOWNS D et al.: Design of potent inhibitors for human brain memapsin 2 (β-secretase). J. Am. Chem. Soc. (2000) 122:3522.
   PubMed Web of Science ®Google Scholar
• RAJAMANI R, REYNOLDS CH: Modeling the binding affinities of β-secretase inhibitors: application to subsite specificity. Bioorg. Med. Chem. Lett. (2004) 14:4843-4846.
   PubMed Web of Science ®Google Scholar
• S-PLUS, Version 6.0; Insightful (2001).
   Google Scholar
• HOLLOWAY MK, MCGAUGHEY GB, COBURN CA et al.: Evaluating scoring functions for docking and designing β-secretase inhibitors. Bioorg. Med. Chem. Lett. (2006) 17:823-827.
   PubMed Web of Science ®Google Scholar
• MCGAUGHEY GB, COLUSSI D, GRAHAM SL et al.: β-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites. Bioorg. Med. Chem. Lett. (2007) 17:1117-1121.
   PubMed Web of Science ®Google Scholar
• BRADY SF, SINGH S, CROUTHAMEL M-C et al.: Rational design and synthesis of selective BACE-1 inhibitors. Bioorg. Med. Chem. Lett. (2004) 14:601-604.
   PubMed Web of Science ®Google Scholar
• TURNER RT, LOY JA, NGUYEN C et al.: Specificity of memapsin 1 and its implication on the design of memapsin 2 (β-secretase) inhibitor selectivity. Biochemistry (2002) 41:8742-8746.
   PubMed Web of Science ®Google Scholar
• DOMINGUEZ D, TOURNOY J, HARTMANN D et al.: Phenotypic and biochemical analyses of BACE1- and BACE2-deficient mice. J. Biol. Chem. (2005) 280:30797-30806.
   PubMed Web of Science ®Google Scholar
• CHOU KC: Insights from modeling the tertiary structure of human BACE2. J. Proteome Res. (2004) 3:1069-1072.
   PubMed Web of Science ®Google Scholar
• CHOU KC, HOWE WJ: Prediction of the tertiary structure of the β-secretase zymogen. Biochem. Biophys. Res. Commun. (2002) 292:702-708.
   PubMed Web of Science ®Google Scholar
• OSTERMANN N, EDER J, EIDHOFF U et al.: Crystal structure of human BACE2 in complex with a hydroxyethylamine transition-state inhibitor. J. Mol. Biol. (2006) 355:249-261.
   PubMed Web of Science ®Google Scholar
• GORFE A, CAFLISCH A: Functional plasticity in the substrate binding site of β-secretase. Structure (2005) 13:1487-1498.
   PubMed Web of Science ®Google Scholar
• XIONG B, HUANG X-Q, SHEN L-L et al.: Conformational flexibility of β-secretase: molecular dynamics simulation and essential dynamics analysis. Acta Phamacol. Sin. (2004) 6:705-713.
   Google Scholar
• MOITESSIER N, THERRIEN E, HANESSIAN S: A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic β-secretase (BACE 1) inhibitors. J. Med. Chem. (2006) 49(20):5885-5894.
   PubMed Web of Science ®Google Scholar
• LIMONGELLI V, MARINELLI L, COSCONATI S: Ensemble-docking approach on BACE-1: pharmacophore perception and guide lines for drug design. Chem. Med. Chem (2007) 2:667-678.
   Google Scholar
• HUANG D, LUTHI U, KOLB P et al.: Discovery of cell-permeable non-peptide inhibitors of β-secretase by high-throughput docking and continuum electrostatics calculations. J. Med. Chem. (2005) 48:5108-5111.
   PubMed Web of Science ®Google Scholar
• RISHTON GM, LABONTE K, WILLIAMS AJ et al.: Computational approaches to the prediction of blood–brain barrier permeability: a comparative analysis of central nervous system drugs versus secretase inhibitors for Alzheimer's disease. Curr. Opin. Drug Discov. Develop. (2006) 9:303-313.
   PubMed Web of Science ®Google Scholar
• RAJAPAKSE HA: The discovery of non transition-state isostere BACE inhibitors. 39th Middle Atlantic Regional Meeting of the American Chemical Society, Collegeville, PA, USA (16 – 18 May 2007).
   Google Scholar
• STAUFFER SR, STANTON MG, GREGRO AR et al.: Discovery and SAR of isonicotinamine BACE-1 inhibitors that bind β-secretase in a N-terminal 10s-loop down conformation. Bioorg. Med. Chem. Lett. (2007) 17:1788-1792.
   PubMed Web of Science ®Google Scholar
• COBURN CA, STACHEL SJ, JONES KG et al.: BACE-1 inhibition by a series of Φ[CH2NH] reduced amide isosteres. Bioorg. Med. Chem. Lett. (2006) 16:3635-3638.
   PubMed Web of Science ®Google Scholar
• STANTON MG, STAUFFER SR, GREGRO AR et al.: Discovery of isonicotinamide derived secretase inhibitors: in vivo reduction of Aβ. J. Med. Chem. (2007) 50:3431-3433.
   PubMed Web of Science ®Google Scholar
• WONG KF, WATNEY JB, HAMMES-SCHIFFER S: Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase. J. Phys. Chem. B. (2004) 108:12231-12241.
   Web of Science ®Google Scholar
• MELNIKOVA I: Therapies for Alzheimer's disease. Nat. Rev. Drug. Dis. (2007) 6:340-341.
   PubMed Web of Science ®Google Scholar
• PyMol, v.99 distributed by DeLano Scientific LLC.
   Google Scholar