Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2005-09-20
2005-09-20
Allen, Marianne P. (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C702S020000, C702S027000
Reexamination Certificate
active
06947845
ABSTRACT:
The invention provides methods for producing high resolution crystals of ribosomes and ribosomal subunits as well as crystals produced by such methods. The invention also provides high resolution structures of ribosomal subunits either alone or in combination with protein synthesis inhibitors. The invention provides methods for identifying ribosome-related ligands and methods for designing ligands with specific ribosome-binding properties as well as ligands that may act as protein synthesis inhibitors. Thus, the methods and compositions of the invention may be used to produce ligands that are designed to specifically kill or inhibit the growth of any target organism.
REFERENCES:
patent: 5180719 (1993-01-01), White et al.
patent: 5281703 (1994-01-01), White et al.
patent: 5336768 (1994-08-01), Albrecht et al.
patent: 5466681 (1995-11-01), Krivan et al.
patent: 5693791 (1997-12-01), Truett
patent: 5866549 (1999-02-01), Or et al.
patent: 5905144 (1999-05-01), Truett
patent: 6380356 (2002-04-01), Griffin et al.
patent: 6437119 (2002-08-01), Truett
patent: 6446032 (2002-09-01), Schimmel
patent: 6468979 (2002-10-01), Pellacini et al.
patent: 2002/0022257 (2002-02-01), Suh et al.
patent: 2002/0086308 (2002-07-01), Steitz et al.
patent: 2002/0188108 (2002-12-01), Noller et al.
patent: 2003/0027315 (2003-02-01), Yonath et al.
patent: 1 172 374 (2002-01-01), None
patent: 1 186 614 (2002-03-01), None
patent: 1 188 769 (2002-03-01), None
patent: WO 95/07271 (1995-03-01), None
patent: WO 96/18633 (1996-06-01), None
patent: WO 97/35195 (1997-09-01), None
patent: WO 99/63937 (1999-12-01), None
patent: WO 00/32619 (2000-06-01), None
patent: WO 01/80863 (2001-11-01), None
Franceshi et al. (1993) “Towards Atomic Resolution of Prokaryotic Ribosomes: Crystallographic, Genetic and Biochemical Studies” inThe Translational Apparatus397-410.
Hope et al. (1989) “Cryocrystallography of Ribosomal Particles”Acta. Cryst. B45: 190-199.
Shevack et al. (1985) “Characterization and Crystallization of Ribosomal Particles fromHalobacterium Marismortui” FEBS Letters184(1):68-71.
Yonath et al. (1980) “Crystallization of the Large Ribosomal Subunits fromBacillus stearothermophilus” Biochem. Intern'l. 1(5): 428-435.
Yonath et al. (1984) “Some X-ray Diffraction Patterns from Single Crystals of the Large Ribosomal Subunit fromBacillus Stearothermophilus” J. Mol. Biol. 177:201-206.
Yonath et al. (1988) “Crystallography of Ribosomal Particles”J. Cryst. Growth90: 231-244.
Hansen et al., “Structural Insights into Peptide Bond Formation,”Proc. Natl. Acad. Sci. USA, 99(18):11670-11675 (2002).
Hansen et al., “The Structures of Four Marcolide Antibiotics Bound to the Large Ribosomal Subunit,”Molecular Cell, 10:117-128 (2002).
Klein et al., “The Kink-Turn: A New RNA Secondary Structure Motif,”EMBO J., 20(15):4214-4221 (2001).
Nissen et al., “RNA Tertiary Interactions in the Large Ribosomal Subunit: The A-Minor Motif,”Proc. Natl. Acad. Sci. USA, 98(9):4899-4903 (2001).
Schmeing et al., “A Pre-Translocational Intermediate in Protein Synthesis Observed in Crystals of Enzymatically Active 50S Subunits,”Nature Struct. Biol., 9(3):225-230 (2002).
Drenth, “Principles of Protein X-ray Crystallography,” 1994, Springer-Verlag, pp. 1-18.
Fourmy et al. (1996) “Structure of the A Site ofEscherichia coli16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic”Science274(5291):1367-1371.
Hermann et al. (1999) “Docking of Cationic Antibiotics to Negatively Charged Pockets on RNA Folds”J. Med. Chem. 42(7):1250-1261.
Ioannou et al. (1998) “Kinetics of Inhibition of Rabbit Reticulocyte Peptidyltransferase by Anisomycin and Sparsomycin”Molecular Pharmacology53(6):1089-1096.
Kirillov et al. (1999) “Peptidyl Transferase Antibiotics Perurb the Relative Positioning of the 3′-Terminal Adenosine of P/P′-Site-Bound tRNA and 23S rRNA in the Ribosome”RNA5(8):1003-1013.
Spickler et al. (1997) “Streptomycin Binds to the Decoding Center of 16 S Ribosomal RNA”J. Mol. Biol. 273(3):586-599.
Wong et al. (1998) “Specificity of Aminoglycoside Antibiotics for the A-Site of the Decoding Region of Ribosomal RNA”Chemistry&Biology5(7):397-406.
Hanessian et al. (1984) “Quantamycin”: A Computer-Stimulated New-Generation Inhibitor of Bacterial Ribosomal BindingJournal American Chemical Society106:6114-6115.
Vince et al. (1975) “Chloramphenicol Binding Site with Analogues of Chloramphenico l and Puromycin”Antimicrobial Agents and Chemotherapy8(4):439-443.
Shuker et al. (1996) “Discovering High-Affinity Ligands for Proteins: SAR by NMR”Science274(5292):1531-1541.
Hecker et al. (1993) “Application of Hygromycin A Structure Activity Relationships to the Antibiotic A201A”Bioorganic&Medicinal Chemistry Letters3(2):295-298.
Wang et al. (1997) “Dimeric Aminoglycosides: Design, Synthesis and RNA Binding”Bioorganic&Medicinal Chemistry Letters7(14):1951-1956.
Holmes et al. (1993) “Novel Dimeric Penicillin Derived Inhibitors of HIV-1 Proteinase: interaction woth the Catalytic Aspartates”Bioorganic&Medicinal Chemistry Letters3(4):503-508.
Rao et al. (1997) “Tight Binding of a Dimeric Derivative of Vancomycin with Dimeric L-Lys-D-Ala-D-Ala”J. Am. Chem. Soc. 119:10286-10290.
Tanihara et al. (1998) “Thrombin-Sensitive Peptide Linkers for Biological Signal-Responsive Drug Release Systems”Peptides19(3):421-425.
Vester et al., (2001) “Macrolide Resistance Conferred by Base Substitutions,”Antimicrobial Agents and Chemotherapyvol. 45, No. 1, pp. 1-12.
Vester et al., (1988) “The Importance of Highly Conserved Nucleotides in the Binding Region of Chloramphenicol at the Peptidyl transfer Centre ofEscherichia coli23S Ribosomal RNA,”The EMBO Journalvol. 7, No. 11, pp. 3577-3587.
Volkmann et al., (1990) “Characterization and Preliminary Crystallographic Studies on Large Ribosomal Subunits fromThermus thermophilus, ”J. Mol. Biol. vol. 216, pp. 239-241.
Von Bohlen, (1991) “Characterization and Preliminary Attempts for Derivatization of Crystals of Large Ribosomal Subunits fromHaloarcula marismortuiDiffracting to 3 Å Resolution,”Journal Molecular Biologyvol. 222, pp. 11-15.
Welch, M., et al., (1997) “23S rRNA Similarity from Selection for Peptidyl Transferase Mimicry,”Biochemistryvol. 36, pp. 6614-6623.
Welch, M., et al., (1995) “An Inhibitor of Ribosomal Peptidyl Transferase Using Transition-State Analogy,”Biochemistryvol. 34, pp. 385-390.
Wimberly, B., et al., (2000) “Structure of the 30S Ribosomal Subunit,”Naturevol. 407, pp. 327-339.
Wittmann et al., (1982) “Crystallization ofEscherichia coliRibosomes,”Febs Lettersvol. 146, No. 1, pp. 217-220.
Wool, I., et al., (1995) “Structure and Evolution of Mammalian Ribosomal Proteins,”Biochemistry Cell Biologyvol. 73, pp. 933-947.
Xiong, L., et al., (2000) “Oxazolidinone Resistance Mutations in 23S rRNA ofEscherichia coliReveal the Central Region of Domain V as the Primary Site of Drug Action,” Journal of Bacteriology vol. 182, No. 19, pp. 5325-5331.
Yonath, A., et al., (1998) “Crystallographic Studies on the Ribosome, a Large Macromolecular Assembly Exhibiting Severe Nonisomorphism, Extreme Beam Sensitivity and No Internal Symmetry,”Acta Cryst, vol. A54, pp. 945-955.
Yonath, A., et al.., (1986) “Characterization of Single Crystals of the Large Ribosomal Particles fromBacillus stearothermophilus,” J. Mol. Biol. vol. 187, pp. 633-636.
Yusupova, G., et al., (2001) “The Path of Messenger RNA through the Ribosome,”Cellvol. 106, pp. 233-241.
Yusupov, M.,et al., (2001) “Crystal Structure of the Ribosome 5.5 Å Resolution,”Sciencevol. 292, pp. 883-896.
Yusupov,
Ban Nenad
Hansen Jeffrey L.
Ippolito Joseph A.
Moore Peter B.
Nissen Poul
Allen Marianne P.
Mahatan Channing S.
Rib-X Pharmaceuticals, Inc.
Testa Hurwitz & Thibeault LLP
Yale University
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