pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition.

BACE1, a major therapeutic target for treatment of Alzheimer's disease, functions within a narrow pH range. Despite tremendous effort and progress in the development of BACE1 inhibitors, details of the underlying pH-dependent regulatory mechanism remain unclear. Here we elucidate the pH-dependent conformational mechanism that regulates BACE1 activity using continuous constant-pH molecular dynamics (MD). The simulations reveal that BACE1 mainly occupies three conformational states and that the relative populations of the states shift according to pH. At intermediate pH, when the catalytic dyad is monoprotonated, a binding-competent state is highly populated, while at low and high pH a Tyr-inhibited state is dominant. Our data provide strong evidence supporting conformational selection as a major mechanism for substrate and peptide-inhibitor binding. These new insights, while consistent with experiment, greatly extend the knowledge of BACE1 and have implications for further optimization of inhibitors and understanding potential side effects of targeting BACE1. Finally, the work highlights the importance of properly modeling protonation states in MD simulations.

[1]  M. Witmer,et al.  Kinetic studies on beta-site amyloid precursor protein-cleaving enzyme (BACE). Confirmation of an iso mechanism. , 2003, The Journal of biological chemistry.

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

[3]  G. Gilliland,et al.  Can enzymes adopt a self-inhibited form? Results of x-ray crystallographic studies of chymosin. , 1992, Biochemical and Biophysical Research Communications - BBRC.

[4]  R. Vassar.  BACE1 inhibitor drugs in clinical trials for Alzheimer’s disease , 2014, Alzheimer's Research & Therapy.

[5]  Jana K. Shen,et al.  Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation. , 2012, Biophysical journal.

[6]  Shankar Venkatraman,et al.  Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. , 2013, Journal of medicinal chemistry.

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

[8]  Nick C Fox,et al.  Clinical and biomarker changes in dominantly inherited Alzheimer's disease. , 2012, The New England journal of medicine.

[9]  Steven A. Spronk,et al.  The role of tyrosine 71 in modulating the flap conformations of BACE1 , 2011, Proteins.

[10]  B. Brooks,et al.  Conformational relaxation and water penetration coupled to ionization of internal groups in proteins. , 2011, The journal of physical chemistry. A.

[11]  C. Brooks,et al.  Constant‐pH molecular dynamics using continuous titration coordinates , 2004, Proteins.

[12]  Wei Chen,et al.  Recent development and application of constant pH molecular dynamics , 2014, Molecular simulation.

[13]  A. Caflisch,et al.  Functional Plasticity in the Substrate Binding Site of β-Secretase , 2005 .

[14]  Takashi Sakurai,et al.  Crystal Structure of an Active Form of BACE1, an Enzyme Responsible for Amyloid β Protein Production , 2008, Molecular and Cellular Biology.

[15]  D. Schlatter,et al.  Substrate and Inhibitor Profile of BACE (β-Secretase) and Comparison with Other Mammalian Aspartic Proteases* , 2002, The Journal of Biological Chemistry.

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

[17]  Patty C. Kandalepas,et al.  Identification and biology of β‐secretase , 2012, Journal of neurochemistry.

[18]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[19]  Jana K. Shen,et al.  Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange. , 2011, Journal of chemical theory and computation.

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

[21]  C. Brooks,et al.  Constant pH molecular dynamics with proton tautomerism. , 2005, Biophysical journal.

[22]  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.

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

[24]  Jana K. Shen,et al.  Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy , 2011, Proteins.

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

[26]  P. Wong,et al.  BACE1 inhibition reduces endogenous Abeta and alters APP processing in wild‐type mice 2 , 2006, Journal of neurochemistry.