Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study
暂无分享,去创建一个
[1] Leighton Coates,et al. X-ray, neutron and NMR studies of the catalytic mechanism of aspartic proteinases , 2006, European Biophysics Journal.
[2] T. Meek,et al. Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. , 1991, Biochemistry.
[3] J. Hardy,et al. Amyloid deposition as the central event in the aetiology of Alzheimer's disease. , 1991, Trends in pharmacological sciences.
[4] J. Åqvist,et al. Catalysis and linear free energy relationships in aspartic proteases. , 2006, Biochemistry.
[5] Tímea Polgár,et al. Virtual screening for beta-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228. , 2005, Journal of medicinal chemistry.
[6] E. Padlan,et al. Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[7] M. Katharine Holloway,et al. BACE-1 inhibition by a series of ψ[CH2NH] reduced amide isosteres , 2006 .
[8] Jan H. Jensen,et al. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. , 2011, Journal of chemical theory and computation.
[9] Jan H. Jensen,et al. Very fast prediction and rationalization of pKa values for protein–ligand complexes , 2008, Proteins.
[10] Kenneth M Merz,et al. Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement. , 2006, Journal of chemical theory and computation.
[11] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[12] D. Northrop,et al. Follow the protons: a low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases. , 2001, Accounts of chemical research.
[13] Erik Lindström,et al. Effect of the protonation state of the titratable residues on the inhibitor affinity to BACE-1. , 2010, Biochemistry.
[14] Charles J. Eyermann,et al. NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor , 1994 .
[15] Gert Vriend,et al. Models@Home: distributed computing in bioinformatics using a screensaver based approach , 2002, Bioinform..
[16] Min Xu,et al. Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1). , 2006, Journal of medicinal chemistry.
[17] David G. Tew,et al. Identification of a Novel Aspartic Protease (Asp 2) as β-Secretase , 1999, Molecular and Cellular Neuroscience.
[18] James E Audia,et al. Robust Central Reduction of Amyloid-β in Humans with an Orally Available, Non-Peptidic β-Secretase Inhibitor , 2011, The Journal of Neuroscience.
[19] D. E. Clark,et al. Outstanding challenges in protein–ligand docking and structure‐based virtual screening , 2011 .
[20] Fredy Sussman,et al. On a possible neutral charge state for the catalytic dyad in β-secretase when bound to hydroxyethylene transition state analogue inhibitors. , 2011, Journal of medicinal chemistry.
[21] Maria Miller,et al. Crystal structure of a retroviral protease proves relationship to aspartic protease family , 1989, Nature.
[22] Jan H. Jensen,et al. Very fast empirical prediction and rationalization of protein pKa values , 2005, Proteins.
[23] J. Hardy,et al. The Amyloid Hypothesis of Alzheimer ’ s Disease : Progress and Problems on the Road to Therapeutics , 2009 .
[24] G. Martin,et al. Gene action in the aging brain: an evolutionary biological perspective , 2002, Neurobiology of Aging.
[25] J. Treanor,et al. Beta-secretase cleavage of Alzheimer's amyloid precursor protein by the transmembrane aspartic protease BACE. , 1999, Science.
[26] David L. Beveridge,et al. Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation , 1993 .
[27] Jan H. Jensen,et al. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. , 2011, Journal of chemical theory and computation.
[28] D. Goodsell,et al. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.
[29] Anton J. Hopfinger,et al. Constructing Protein Models for Ligand-Receptor Binding Thermodynamic Simulations: An Application to a Set of Peptidometic Renin Inhibitors , 1997, J. Chem. Inf. Comput. Sci..
[30] Hege S. Beard,et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.
[31] D. Davies,et al. The structure and function of the aspartic proteinases. , 1990 .
[32] Jon Cooper,et al. The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. , 2008, Journal of the American Chemical Society.
[33] Arun K. Ghosh,et al. β-Secretase as a therapeutic target for Alzheimer’s disease , 2008, Neurotherapeutics.
[34] C. Dingwall,et al. Second generation of BACE-1 inhibitors part 3: Towards non hydroxyethylamine transition state mimetics. , 2009, Bioorganic & medicinal chemistry letters.
[35] H. Cai,et al. BACE1 is the major β-secretase for generation of Aβ peptides by neurons , 2001, Nature Neuroscience.
[36] Charles H. Reynolds,et al. Modeling the Protonation States of the Catalytic Aspartates in β-Secretase , 2004 .
[37] Fiona Crawford,et al. Soluble Alzheimers β-amyloid constricts the cerebral vasculature in vivo , 1998, Neuroscience Letters.
[38] Romano Silvestri,et al. Boom in the development of non‐peptidic β‐secretase (BACE1) inhibitors for the treatment of Alzheimer's disease , 2009, Medicinal research reviews.
[39] Matthew P. Repasky,et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.
[40] Wei Yang,et al. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems , 2008, Proceedings of the National Academy of Sciences.
[41] R. Barbour,et al. Purification and cloning of amyloid precursor protein β-secretase from human brain , 1999, Nature.
[42] A. Stamford,et al. Potent pyrrolidine- and piperidine-based BACE-1 inhibitors. , 2008, Bioorganic & medicinal chemistry letters.
[43] Ricardo L. Mancera,et al. Ligand-Protein Cross-Docking with Water Molecules , 2010, J. Chem. Inf. Model..
[44] Jian Sun,et al. Fragment-based discovery of nonpeptidic BACE-1 inhibitors using tethering. , 2009, Biochemistry.
[45] Yuan Cheng,et al. From fragment screening to in vivo efficacy: optimization of a series of 2-aminoquinolines as potent inhibitors of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1). , 2011, Journal of medicinal chemistry.
[46] Arghya Barman,et al. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. , 2011, Biochemistry.
[47] L Hong,et al. Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. , 2000, Science.
[48] Hwangseo Park,et al. Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. , 2003, Journal of the American Chemical Society.
[49] Arghya Barman,et al. Computational insights into aspartyl protease activity of presenilin 1 (PS1) generating Alzheimer amyloid beta-peptides (Abeta40 and Abeta42). , 2009, The journal of physical chemistry. B.
[50] E. Koo,et al. Amyloid Precursor Protein Trafficking, Processing, and Function* , 2008, Journal of Biological Chemistry.
[51] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[52] M. Citron,et al. Emerging Alzheimer’s disease therapies: inhibition of β-secretase , 2002, Neurobiology of Aging.
[53] Arghya Barman,et al. Loss of Cleavage at β′-Site Contributes to Apparent Increase in β-Amyloid Peptide (Aβ) Secretion by β-Secretase (BACE1)-Glycosylphosphatidylinositol (GPI) Processing of Amyloid Precursor Protein* , 2011, The Journal of Biological Chemistry.
[54] David S. Goodsell,et al. Grid-Based Hydrogen Bond Potentials with Improved Directionality , 2004 .
[55] Matthew P. Repasky,et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.
[56] Joanna Trylska,et al. The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV‐1 protease , 2004, Protein science : a publication of the Protein Society.
[57] Alfredo G. Tomasselli,et al. Membrane-anchored aspartyl protease with Alzheimer's disease β-secretase activity , 1999, Nature.
[58] Bernard R. Brooks,et al. HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential , 1998 .
[59] Ursula Rothlisberger,et al. Reaction Mechanism of HIV-1 Protease by Hybrid Car-Parrinello/Classical MD Simulations , 2004 .
[60] T. Pillot,et al. The nonfibrillar amyloid beta-peptide induces apoptotic neuronal cell death: involvement of its C-terminal fusogenic domain. , 2002, Journal of neurochemistry.
[61] R. Godemann,et al. Fragment-based discovery of BACE1 inhibitors using functional assays. , 2009, Biochemistry.
[62] Ursula Rothlisberger,et al. Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. , 2005 .
[63] D. Selkoe,et al. Translating cell biology into therapeutic advances in Alzheimer's disease , 1999, Nature.
[64] Lin Hong,et al. Design, synthesis, and X-ray structure of potent memapsin 2 (beta-secretase) inhibitors with isophthalamide derivatives as the P2-P3-ligands. , 2007, Journal of medicinal chemistry.
[65] W. Richards,et al. Mice deficient in BACE1, the Alzheimer's β-secretase, have normal phenotype and abolished β-amyloid generation , 2001, Nature Neuroscience.
[66] Jian Sun,et al. Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1. , 2006, Journal of medicinal chemistry.