Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study

In this molecular docking study, the protonation states of the catalytic Asp dyad of the beta-secretase (BACE1) enzyme in the presence of eight chemically diverse inhibitors have been predicted. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely considered as a promising therapeutic target. All the inhibitors were redocked into their corresponding X-ray structures using a combination of eight different protonation states of the Asp dyad for each inhibitor. Five inhibitors were primarily found to favor two different monoprotonated states, and the remaining three favor a dideprotonated state. In addition, five of them exhibited secondary preference for a diprotonated state. These results show that the knowledge of a single protonation state of the Asp dyad is not sufficient to search for the novel inhibitors of BACE1 and the most plausible state for each inhibitor must be determined prior to conducting in-silico screening.

[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.