Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving antigen-antibody binding – specific binding protein...
Reexamination Certificate
2004-12-20
2010-02-16
Steadman, David J (Department: 1656)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving antigen-antibody binding, specific binding protein...
C702S027000, C703S011000, C435S004000, C435S007400, C435S007600, C435S183000, C435S195000
Reexamination Certificate
active
07662581
ABSTRACT:
This invention provides methods of identifying an Eg5 binding ligand. The ligand is identified by using the atomic coordinates of an Eg5 crystal to generate a three dimensional structure. The three dimensional structure is used in molecular modeling techniques and docking experiments to identify ligands that bind to the binding pocket of Eg5. A novel binding pocket is identified. The invention also provides a crystallized Eg5 and ligand complex.
REFERENCES:
patent: 6207403 (2001-03-01), Goldstein et al.
patent: 6472521 (2002-10-01), Uhlmann et al.
patent: WO 01/30768 (2001-05-01), None
patent: WO 01/98278 (2001-12-01), None
patent: WO 02/056880 (2002-07-01), None
patent: WO 02/057244 (2002-07-01), None
patent: WO 02/078639 (2002-10-01), None
patent: WO 03/039460 (2003-05-01), None
patent: WO 2004/004652 (2004-01-01), None
Ngo et al. in The Protein Folding Problem and Tertiary Structure Prediction, 1994, Merz et al. (ed.), Birkhauser, Boston, MA, pp. 433 and 492-495.
Turner et al., J. Biol. Chem., 2001, 276(27):25496-25502.
Hopkins et al., Biochemistry, 2000, 39(10):2805-14.
Witkowski et al., Biochemistry, 38, 11643-11650, 1999.
Wishart et al., Journal of Biological Chemistry, vol. 270, No. 45, pp. 26782-26785, 1995.
Kisselev, Structure, vol. 10, pp. 8-9, 2002.
Branden et al., “Introduction to Protein Structure Second Edition”, Garland Publishing Inc., New York, 1999.
Drenth, “Principles of X-ray Crystallography,” Springer, New York, 1995.
Kierzek et al., Biophys Chem 91:1-20, 2001.
U.S. Appl. No. 60/480,180, filed Jun. 20, 2003, Wang, et al.
U.S. Appl. No. 60/580,927, filed Jun. 18, 2004, Barsanti, et al.
U.S. Appl. No. 60/620,385, filed Oct. 19, 2004, Boyce, et al.
Blaney, et al., “A good ligand is hard to find: Automated docking methods”,Perspectives in Drug Discovery and Design, 1:301-319 (1993).
Blangy, et al., “Phosphorylation by p34cdc2Regulates Spindle Association of Human Eg5, a Kinesin-Related Motor Essential for Bipolar Spindle Formation in Vivo”,Cell, 83:1159-1169, (1995).
Böhm, “The computer program LUDI: A new method for the de novo design of enzyme inhibitors”,J. Comp. Aided Molec. Design, 6:61-78, (1992).
Caflisch, et al., “Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase”,J. Med. Chem., 36(15):2142-67, (1993).
DeBonis, et al., “Interaction of the Mitotic Inhibitor Monastrol with Human Kinesin Eg5”,Biochemistry, 42(2):338-349, (2003).
Eisen, et al., “HOOK: A Program for Finding Novel Molecular Architectures That Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site”,Proteins: Str. Funct. Genet., 19:199-221, (1994).
Enos, et al., “Mutation of a Gene That Encodes a Kinesin-like Protein Blocks Nuclear Division in A. nidulans”,Cell, 60:1019-1027, (1990).
Gehlhaar, et al., “De NovoDesign of Enzyme Inhibitors by Monte Carlo Ligand Generation”,J. Med. Chem., 38:466-72, (1995).
Giet, et al., “TheXenopus laevisAurora-related Protein Kinase pEg2 Associates with and Phosphorylates the Kinesin-related Protein XIEg5”,J. Biol. Chem., 274(21):15005-15013, (1999).
Goodsell, et al., “Automated Docking of Substrates to Proteins by Simulated Annealing”,Proteins: Str. Funct Genet., 8:195-202, (1990).
Hagan, et al., “Novel potential mitotic motor protein encoded by the fission yeastcut7+ gene”,Nature, 347:563-566, (1990).
Jones, et al., “Development and Validation of a Genetic Algorithm for Flexible Docking”,J. Mol. Biol., 267:727-748, (1997).
Kaiser, et al., “All-trans-Retinoic Acid-mediated Growth Inhibition Involves Inhibition of Human Kinesin-related Protein HsEg5”,J. Biol. Chem., 274(27):18925-18931, (1999).
Kapoor, et al., “Probing Spindle Assembly Mechanisms with Monastrol, a Small Molecule Inhibitor of the Mitotic Kinesin, Eg5”,J. Cell Biol., 150(5):975-988, (2000).
Kuntz, et al., “A Geometric Approach to Macromolecule-Ligand Interactions”,J. Mol. Biol., 161:269-288, (1982).
Lauri, et al., “CAVEAT: A program to facilitate the design of organic molecules”,J. Comp. Aided Mol. Design, 8:51-66, (1994).
Luo, et al., “RASSE: A New Method for Structure-Based Drug Design”,J. Chem. Inf. Comput. Sci., 36:1187-1194, (1996).
Martin, “3D Database Searching in Drug Design”,J. Med. Chem., 35(12):2145-54, (1992).
Mayer, et al., “Small Molecule Inhibitor of Mitotic Spindle Bipolarity Identified in a Phenotype-Based Screen”,Science286:971-974, (1999).
Meyer, et al., “Backward binding and other structural surprises”,Perspectives in Drug Disc. and Design, 3:168-95, (1995).
Moon, et al., “Computer Design of Bioactive Molecules: A Method for Receptor-Based de Novo Ligand Design”,Proteins: Str. Funct. Genet., 11:314-328, (1991).
Nicklaus, et al., “Conformational Changes of Small Molecules Binding to Proteins”,Bioorganic&Medicinal Chemistry, 3(4):411-428, (1995).
Rotstein, et al., “GroupBuild: A Fragment-Based Method forDe NovoDrug Design”, J.Med. Chem., 36:1700-1710, (1993).
Turner, et al., “Crystal Structure of the Mitotic Spindle Kinesin Eg5 Reveals a Novel Conformation of the Neck-linker”,J. Biol. Chem., 276(27):25496-25502, (2001).
Bussiere Dirksen
Knapp Mark
Le Vincent P.
Martin Eric
Kathardekar Vinit
Lee Jae W
Novartis Vaccines and Diagnostics Inc.
Steadman David J
Tanner Lorna
LandOfFree
Eg5 co-crystals does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Eg5 co-crystals, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Eg5 co-crystals will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4181161