Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Chemical analysis
Reexamination Certificate
2007-05-08
2007-05-08
Allen, Marianne P. (Department: 1647)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Chemical analysis
C702S019000, C702S020000
Reexamination Certificate
active
09678016
ABSTRACT:
The present invention relates to a data storage medium encoded with the corresponding structure coordinates of molecules and molecular complexes which comprise the active site binding pockets of IMPDH. Such data storage material is capable of displaying such molecules and molecular complexes, or their structural homologues, as a graphical three-dimensional representation on a computer screen. 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 and design compounds, including inhibitory compounds, that bind to IMPDH or homologues thereof. This invention also relates to molecules and molecular complexes which comprise the active site binding pockets of IMPDH or close structural homologues of the active site binding pockets. This invention also relates to compounds and pharmaceutical compositions which are inhibitors of IMPDH.
REFERENCES:
patent: 4833233 (1989-05-01), Carter
patent: 5353236 (1994-10-01), Subbiah
patent: 5380879 (1995-01-01), Sjogren
patent: 5444072 (1995-08-01), Patterson et al.
patent: 5557535 (1996-09-01), Srinivasan et al.
patent: 5932600 (1999-08-01), Saunders et al.
patent: WO 90/01545 (1990-02-01), None
patent: WO 94/01105 (1994-01-01), None
patent: WO 94/12184 (1994-06-01), None
patent: WO 94/17185 (1994-08-01), None
patent: WO 94/25860 (1994-11-01), None
H.J. Bohm, “The Computer Program LUDI: A New Method For The De Novo Design of Enzyme Inhibitors”,Journal of Computer-Aided Molecular Design, 6, pp. 61-78 (1992).
P.N. Bryan, “Protein Engineering”,Biotech Adv., 5, pp. 221-234 (1987).
I.D. Campbell et al., “Diffraction, in Biological Spectroscopy”,The Benjamin/Cummings Publishing Company, Inc., Menlo Park, CA, pp. 299-326 (1984).
N. Claude Cohen et al., “Molecular Modeling Software and Methods for Medicinal Chemistry”,Journal of Medicinal Chemistry, 33(3), pp. 883-894 (1990).
C.R. Gregory et al., “Treatment With Rapamycin and Mycophenolic Acid Reduces Arterial Intimal Thickening Produced by Mechanical Injury and Allows Endothelial Replacement”,Transplantation, 59(5), pp. 655-661 (Mar. 1995).
C. Hansch et al., “Comparison of the Inhibition ofEscherichia coliandLactobacillus caseiDihydrofolate Reductase by 2,4-diamino-5-(substituted-benzyl) pyrimidines; quantitative Structure-Activity Relationships, X-Ray Crystallography and Computer Graphics in Structure-Activity Analysis”,Chemical Abstracts, 97:298f, p. 29 (1982);Journal of Medicinal Chemistry, 25, pp. 777-784 (1982).
J.A. Huete-Pérez et al., “Identification of the IMP Binding Site in the IMP Dehydrogenase FromTritrichomonas foetus”, Biochemistry, 34(42), pp. 13889-13894 (1995).
J. Jancarik et al., “Sparse Matrix Sampling: A Screening Method for Crystallization of Proteins”,J. Appl. Cryst., 24, pp. 409-411 (1991).
A. Kajihara et al., “Protein Modelling Using a Chimera Reference Protein Derived From Exons”,Protein Eng'g, 6, pp. 615-620 (1993).
R. Li, et al., “A comparison by QSAR, Crystallography, and Computer Graphics of the Inhibition of Various Dihydrofolate Reductases by 5-(x-benzyl)-2,4-diaminopyrimidines”,Chemical Abstracts, 98:172570a, p. 28 (1983);Quantitative Structure Activity Relationships Pharmacol. Chem. Biol., 1, pp. 1-7 (1982).
G.M. Makara et al., “Nuclear Magnetic Resonance and Molecular Modeling Study on Mycophenolic Acid: Implications for Binding to Inosine Monophosphate Dehydrogenase”,J. Med. Chem., 39(6), pp. 1236-1242 (1996).
Y.C. Martin, “3D Database Searching In Drug Design”,Journal of Medicinal Chemistry, 35 (12), pp. 2145-2154 (Jun. 12, 1992).
C. Montero et al., “Demonstration of Induction of Erythrocyte Inosine Monophospate Dehydrogenase Activity in Ribavirin-Treated Patients Using a High Performance Liquid Chromatography Linked Method”,Clinica Chimica Acta, 238, pp. 169-178 (1995).
J.B. Moon et al., “Computer Design of Bioactive Molecules: A Method for Receptor-Based De Novo Ligand Design”, Proteins: Structure, Function, and Genetics, 11, pp. 314-328 (1991).
R.E. Morris, “New Small Molecule Immunosuppressants for Transplantation: Review of Essential Concepts”,The Journal of Heart and Lung Transplantation, Nov./Dec., pp. S275-S286 (1993).
D. Musil et al., “The refined 2.15 Å X-ray crystal structure of human liver cathepsin B: the structural basis for its specificity”,EMBO J., 10(9), pp. 2321-2330 (1991).
A.J. Rusell et al., “Rational Modification of Enzyme Catalysis by Engineering Surface Charge”,Nature, 328, pp. 496-500 (Aug. 6, 1987).
A.R. Sielecki et al., “Structure of Recombinant Human Renin, a Target for Cardiovascular-Active Drugs, at 2.5 Å Resolution”,Science, 243, pp. 1346-1351 (Mar. 1989).
M.D. Sintchak et al., “Structure and Mechanism of Inosine Monophosphate Dehydrogenase in Complex with the Immunosuppressant Mycophenolic Acid”,Cell, 85, pp. 921-930 (Jun. 14, 1996).
U. Uhlin et al., “Crystallization and crystallographic investigations of ribonucleotide reductase protein R1 fromEscherichia coli”, Federation of European Biochemical Societies, 336(1), pp. 148-152 (1993).
F.G. Whitby et al., “Preliminary X-Ray Crystallographic Analysis ofTritrichomonas foetusInosine-5′-Monophosphate Dehydrogenase”,Proteins: Structure, Function, and Genetics, 23, pp. 598-603 (1995).
C.S. Wright et al., “Structure of Subtilisin BPN' at 2.5 Å Resolution”,Nature, 221, pp. 235-242 (Jan. 18, 1969).
Balbes, L.M. et al., “A Perspective of Modern Methods in Computer-Aided Drug Design,” inReviews in Computational Chemistry, K.B. Lipkowitz and D.B. Boyd, Eds., VCH Publishers, New York, 5, pp. 337-379 (1994).
Bartlett, P.A. et al., “CAVEAT: A Program to Facilitate the Structure-Derived Design of Biologically Active Molecules,” inMolecular Recognition in Chemical and Biological Problems, S.M. Roberts, Ed., Royal Society of Chemistry, Special Publication No. 78, pp. 182-196 (1989).
Eisen, M.B. et al., “HOOK: A Program for Finding Novel Molecular Architectures that Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site,”Proteins Struct. Funct. Genet., 19, pp. 199-221 (1994).
Gillet, V. et al., “SPROUT: A Program for Structure Generation,”J. Comp. Aid. Molec. Design, 7, pp. 127-153 (1993).
Goodford, P.J., “A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules,”J. Med. Chem., 28, pp. 849-857 (1985).
Goodsell, D.S. et al., “Automated Docking of Substrates to Proteins by Simulated Annealing,”Proteins Struct. Funct. Genet., 8, pp. 195-202 (1990).
Guida, W.C., “Software for Structure-Based Drug Design,”Curr. Opin. Struct. Biology, 4, pp. 777-781 (1994).
Kuntz, I.D. et al., “A Geometric Approach to Macromolecule-Ligand Interactions,”J. Mol. Biol., 161, pp. 269-288 (1982).
Lauri, G. and Bartlett, P.A., “CAVEAT: A Program to Facilitate the Design of Organic Molecules,”J. Comp. Aid. Molec. Design, 8, pp. 51-66 (1994).
Miranker, A. and Karplus, M., “Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method,”Proteins Struct. Funct. Genet., 11, pp. 29-34 (1991).
Meng, E.C. et al., “Automated Docking with Grid-Based Energy Evaluation,”Journal of Computational Chemistry, 13, pp. 505-524 (1992).
Navia, M.A. and Murcko, M.A., “Use of Structural Information in Drug Design,”Current Opinion in Structural Biology, 2, pp. 202-210 (1992).
Nishibata, Y. and Itai, A., “Automatic Creation of Drug Candidate Structures Based on Receptor Structure. Starting Point for Artificial Lead Generation,” Tetrahedron, 47, pp. 8985-8990 (1991).
Armistead David M.
Fleming Mark Andrew
Sintchak Michael D.
Wilson Keith P.
Allen Marianne P.
Fish & Neave IP Group Ropes & Gray LLP
Haley James F.
Vertex Pharmaceuticals Incorporated
LandOfFree
Methods of using the structure coordinates of molecules... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods of using the structure coordinates of molecules..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods of using the structure coordinates of molecules... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3791795