Crystal structure of Rho-kinase I kinase domain complexes...

Details Crystal structure of Rho-kinase I kinase domain complexes... Crystal structure of Rho-kinase I kinase domain complexes...

2006-06-28

2010-02-02

Noakes, Suzanne M. (Department: 1656)

Chemistry: molecular biology and microbiology

Enzyme , proenzyme; compositions thereof; process for...

C436S004000

Reexamination Certificate

active

07655446

ABSTRACT:
The present invention relates to human Rho-kinase I (ROCK I), ROCK I binding pockets, ROCK I-like binding pockets. More particularly, the present invention provides a computer comprising a data storage medium encoded with the structure coordinates of such binding pockets. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for and design compounds, including inhibitory compounds, that bind to ROCK I protein or ROCK I protein homologues, or complexes thereof. The invention also relates to crystallizable compositions and crystals comprising ROCK I kinase domain and ROCK I kinase domain complexed with an inhibitor of that domain. The invention also relates to methods of identifying inhibitors of the ROCK I kinase domain.

REFERENCES:
patent: 4886646 (1989-12-01), Carter et al.
patent: 5096676 (1992-03-01), McPherson et al.
patent: 5130105 (1992-07-01), Carter et al.
patent: 5221410 (1993-06-01), Kushner et al.
patent: 5400741 (1995-03-01), DeTitta et al.
patent: 5884230 (1999-03-01), Srinivasan et al.
McPherson Eur. J. Biochem. 1990, 189:1-23.
Kundrot et al. Cell. Mol. Life Sci. 2004, 61: 525-536.
Benevenuti et al., Nature Protocols, published on-line Jun. 28, 2007, 2(7):1633-1651.
R. Cudney, Rigaku Journal, 1999, vol. 16, No. 1, pp. 1-7.
Drenth, “Principles of Protein X-Ray Crystallography”, 2nd Edition, 1999 Springer-Verlag New York Inc., Chapter 1, p. 19, 4th paragraph, lines 1-2.
Amano et al., “Phosphorylation and Activation of Myosin by Rho-associated Kinase (Rho-Kinase),”The Journal of Biological Chemistry, 271(34):20246-20249 (1996).
Amano et al., “Myosin II Activation Promotes Neurite Retraction during the Action of Rho and Rho-kinase,”Genes to Cells, 3:177-188 (1998).
Amano et al., The COOH Terminus of Rho-Kinase Negatively Regulates Rho-Kinase Activity,The Journal of Biological Chemistry, 274(45):32418-32424 (1999).
Balbes et al., “A Perspective of Modern Methods in Computer-Aided Drug Design,”Reviews in Computational Chemistry, K.B. Lipkowitz and D.B. Boyd Eds., VCH Publishers, New York, 5:337-379 (1994).
Bartlett et al., “CAVEAT: A Program to Facilitate the Structure-derived Design of Biologically Active Molecules,”Molecular Recognition in Chemical and Biological Problems, S.M. Roberts, Ed., Royal Society of Chemistry, 78:182-196 (1989).
Blundell et al., “Knowledge-based Prediction of Protein Structures and the Design of Novel Molecules,”Nature, 326:347-352 (1987).
Böhm, “The Computer Program LUDI: A New Method for thede novoDesign of Enzyme Inhibitors,”Journal of Computer-Aided Molecular Design, 6:61-78 (1992).
Breitenlechner et al., “Protein Kinase A in Complex with Rho-Kinase Inhibitors Y-27632, Fasudil, and H-1152P: Structural Basis of Selectivity,”Structure, 11:1595-1607 (2003).
Brünger et al., “Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination,”Acta Crystallographica, D54:905-921, (1998).
Carson, “Ribbons 2.0,”Journal of Applied Crystallography, 24:958-961 (1991).
Chambers et al., “High-throughout Screening for Soluble Recombinant Expressed Kinases inEscherichia coliand Insect Cells,”Protein Expression and Purification, 36:40-47 (2004).
Chayen, “A Novel Technique to Control the Rate of Vapour Diffusion, Giving Larger Protein Crystals,”Journal of Applied Crystallography, 30:198-202 (1997).
Cohen et al., “Molecular Modeling Software and Methods for Medicinal Chemistry,”Journal of Medicinal Chemistry, 33(3):883-894 (1990).
Cory and Bentley, “MATCHMOL, an Interactive Computer Graphics Procedure for Superposition of Molecular Models,”Journal of Molecular Graphics, 2:39-42 (1984).
D'Arcy et al., “A Novel Approach to Crystallising Proteins under Oil,”Journal of Crystal Growth, 168:175-180 (1996).
Dayhoff et al., “A Model of Evolutionary Change in Proteins,”Atlas of Protein Sequence and Structure, 5(3):345-352 (1978).
Doran et al., “New Insights into the Structure-Function Relationships of Rho-associated Kinaså: A Thermodynamic and Hydrodynamic Study of the Dimer-to-Monomer Transition and its Kinetic Implications,”Biochemical Journal, 384:255-262 (2004).
Eisen et al., “HOOK: A Program for Finding Novel Molecular Architectures that Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site,”Proteins: Structure, Functions and Genetics, 19:199-221 (1994).
Fetrow and Bryant, “New Programs for Protein Tertiary Structure Prediction,”Bio/Technology, 11:479-484 (1993).
Fox et al., “A Single Amino Acid Substitution Makes ERK2 Susceptible to Pyridinyl Imidazole Inhibitors of p38 MAP Kinase,”Protein Science, 7, 2249-2255 (1998).
Gillet et al., “SPROUT: A Program for Structure Generation,”Journal of Computer-Aided Molecular Design, 7:127-153 (1993).
Goodford, “A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules,”Journal of Medicinal Chemistry, 28:849-857 (1985).
Goodsell and Olson, “Automated Docking of Substrates to Proteins by Simulated Annealing,”Proteins: Structure, Function and Genetics, 8:195-202 (1990).
Greer, “Comparative Modeling of Homologous Proteins,”Methods in Enzymology, 202:239-252 (1991).
Gschwend et al., “Molecular Docking Towards Drug Discovery,”Journal of Molecular Recognition, 9:175-186 (1996).
Guex and Peitsch, “Swiss-Model: and the Swiss-PdbViewer: An Environment for Comparative Protein Modeling,”Electrophoresis, 18:2714-2723 (1997).
Guida, “Software for Structured-based Drug Design,”Current Opinion in Structural Biology, 4:777-781 (1994).
Hammond et al., “Characterization of Two Alternately Spliced Forms of Phospholipase D1,”The Journal of Biological Chemistry, 272(6):3860-3868 (1997).
Hanks et al., “The Protein Kinase Family: Conserved Features and Deduced Phylogeny of the Catalytic Domains,”Science, 241:42-52 (1988).
Hanks and Quinn, “Protein Kinase Catalytic Domain Sequence Database: Identification of Conserved Features of Primary Structure and Classification of Family Members,”Methods in Enzymology, 200:38-62 (1991).
Higgins et al., “Using CLUSTAL for Multiple Sequence Alignments,”Methods in Enzymology, 266:383-402 (1996).
Hirose et al., “Molecular Discussion of the Rho-associated Protein Kinase (p160ROCK)-regulated Neurite Remodeling in Neuroblastoma N1E-115 Cells,”The Journal of Cell Biology, 141(7):1625-1636 (1998).
Ishizaki et al., “p160ROCK, a Rho-associated Coiled-coil Forming Protein Kinase, Works Downstream of Rho and Induces Focal Adhesions,”FEBS Letters, 404:118-124 (1997).
Johnson et al., “Knowledge-Based Protein Modeling,”Critical Reviews in Biochemistry and Molecular Biology. 29:1-68 (1994).
Jones et al., “Improved Methods for Building Protein Models in Electron Density Maps and the Location of Errors in these Models,”Acta Crystallographica, A47:110-119 (1991).
Kawano et al., “Phosphorylation of Myosin-binding Subunit (MBS) of Myosin Phosphatase by Rho-Kinase In Vivo,”The Journal of Cell Biology, 147(5):1023-1037 (1999).
Kuntz et al., “A Geometric Approach to Macromolecule-Ligand Interactions,”The Journal of Molecular Biology, 161:269-288 (1982).
Kureishi et al., “Rho-associated Kinase Directly Induces Smooth Muscle Contraction through Myosin Light Chain Phosphorylation,”The Journal of Biological Chemistry, 272(19):12257-12260 (1997).
Lattman, “Use of the Rotation and Translation Functions,”Methods in Enzymology, 115:55-77 (1985).
Lauri and Bartlett, “CAVEAT: A Program to F

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