Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.

[1]  R. Engh,et al.  Structural aspects of protein kinase control-role of conformational flexibility. , 2002, Pharmacology & therapeutics.

[2]  J Moult,et al.  Analysis of the steric strain in the polypeptide backbone of protein molecules , 1991, Proteins.

[3]  Valerie Daggett,et al.  Molecular dynamics simulations of the protein unfolding/folding reaction. , 2002, Accounts of chemical research.

[4]  Luping Liu,et al.  Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase. , 2003, Bioorganic & medicinal chemistry letters.

[5]  S. Nosé A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[6]  J. Mongan,et al.  Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.

[7]  K. Tai Conformational sampling for the impatient. , 2004, Biophysical chemistry.

[8]  E. Goldsmith,et al.  The structure of mitogen-activated protein kinase p38 at 2.1-A resolution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Viktor Hornak,et al.  Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations. , 2004, Journal of molecular graphics & modelling.

[10]  Malin M. Young,et al.  Predicting conformational switches in proteins , 1999, Protein science : a publication of the Protein Society.

[11]  I. Luque,et al.  Structural stability of binding sites: Consequences for binding affinity and allosteric effects , 2000, Proteins.

[12]  S. Teague Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.

[13]  D. Jacobs,et al.  Protein flexibility predictions using graph theory , 2001, Proteins.

[14]  Martin Zacharias,et al.  Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP , 2004, Proteins.

[15]  V. Daggett Molecular dynamics simulations of the protein unfolding/folding reaction. , 2002, Accounts of chemical research.

[16]  L. Wodicka,et al.  A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.

[17]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[18]  J. Boehm,et al.  p38 MAP kinases: key signalling molecules as therapeutic targets for inflammatory diseases , 2003, Nature Reviews Drug Discovery.

[19]  P. Kollman,et al.  Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .

[20]  J. Warmus,et al.  Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition , 2004, Nature Structural &Molecular Biology.

[21]  E. Goldsmith,et al.  Structural basis of inhibitor selectivity in MAP kinases. , 1998, Structure.

[22]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[23]  Janet M Thornton,et al.  Ligand selectivity and competition between enzymes in silico , 2004, Nature Biotechnology.

[24]  Natasja Brooijmans,et al.  Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.

[25]  J. Wells,et al.  Searching for new allosteric sites in enzymes. , 2004, Current opinion in structural biology.

[26]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[27]  Haruki Nakamura,et al.  A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor , 2004, J. Comput. Chem..

[28]  Gang Liu,et al.  Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. , 2003, Journal of the American Chemical Society.

[29]  William J. Welsh,et al.  Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring. , 2004 .

[30]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[31]  J. Thornton,et al.  Searching for functional sites in protein structures. , 2004, Current opinion in chemical biology.

[32]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[33]  J. Thornton,et al.  A revised set of potentials for beta-turn formation in proteins. , 1994, Protein science : a publication of the Protein Society.

[34]  D. Sept,et al.  Localization of the antimitotic peptide and depsipeptide binding site on beta-tubulin. , 2004, Biochemistry.

[35]  Yuan-Ping Pang,et al.  Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program , 1994, J. Comput. Aided Mol. Des..

[36]  L. Johnson,et al.  Protein Kinase Inhibitors: Insights into Drug Design from Structure , 2004, Science.

[37]  Michelle Browner,et al.  Design and synthesis of 4-azaindoles as inhibitors of p38 MAP kinase. , 2003, Journal of medicinal chemistry.

[38]  James R Horn,et al.  Allosteric inhibition through core disruption. , 2004, Journal of molecular biology.

[39]  L. Tong,et al.  Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site , 2002, Nature Structural Biology.

[40]  Viktor Hornak,et al.  Improved conformational sampling through an efficient combination of mean-field simulation approaches , 2004 .

[41]  S. J. Campbell,et al.  Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.

[42]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[43]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[44]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[45]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[46]  W Patrick Walters,et al.  A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.

[47]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[48]  Gerhard Klebe,et al.  Probing flexibility and “induced‐fit” phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations , 2004, Proteins.

[49]  E. Jaeger,et al.  Docking: successes and challenges. , 2005, Current pharmaceutical design.

[50]  J. Kuriyan,et al.  The Conformational Plasticity of Protein Kinases , 2002, Cell.

[51]  A. Elcock Prediction of functionally important residues based solely on the computed energetics of protein structure. , 2001, Journal of molecular biology.

[52]  Yuan-Ping Pang,et al.  Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies , 1994, J. Comput. Aided Mol. Des..

[53]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[54]  J. Thornton,et al.  Conformational changes observed in enzyme crystal structures upon substrate binding. , 2005, Journal of molecular biology.

[55]  F. Bushman,et al.  Developing a dynamic pharmacophore model for HIV-1 integrase. , 2000, Journal of medicinal chemistry.

[56]  Ruben Abagyan,et al.  Comparative study of several algorithms for flexible ligand docking , 2003, J. Comput. Aided Mol. Des..

[57]  Dino Moras,et al.  Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor , 2003, Nature.

[58]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[59]  A. W. Schüttelkopf,et al.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.

[60]  J Andrew McCammon,et al.  Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach , 2003, Protein science : a publication of the Protein Society.

[61]  C. Pargellis,et al.  The kinetics of binding to p38MAP kinase by analogues of BIRB 796. , 2003, Bioorganic & medicinal chemistry letters.