Chemistry: analytical and immunological testing – Nuclear magnetic resonance – electron spin resonance or other...
Reexamination Certificate
2007-02-20
2007-02-20
Le, Long V. (Department: 1641)
Chemistry: analytical and immunological testing
Nuclear magnetic resonance, electron spin resonance or other...
C435S007100, C435S007920, C436S175000, C436S536000, C436S063000
Reexamination Certificate
active
10087602
ABSTRACT:
Methods and compositions are described for analyzing complex protein mixtures, such as proteomes, using activity-based probes. In particular, probes that specifically react with and bind to the active form of one or more target proteins are employed. Labeled peptides obtained from the labeled active target proteins can be used in screening and identification procedures, and can be related to the identity, presence, amount, or activity of active members of the desired target protein class. The methods and compositions described herein can be used, for example, to provide diagnostic information concerning pathogenic states, in identifying proteins that may act as therapeutic targets, and in drug discovery.
REFERENCES:
patent: 4415655 (1983-11-01), de Castro et al.
patent: 4433051 (1984-02-01), Gilad et al.
patent: 4481094 (1984-11-01), de Castro et al.
patent: 4865707 (1989-09-01), Karger et al.
patent: 4946794 (1990-08-01), Berube
patent: 5041538 (1991-08-01), Ling et al.
patent: 5290920 (1994-03-01), Sindrey et al.
patent: 5856082 (1999-01-01), Aebersold et al.
patent: 6008373 (1999-12-01), Waggoner et al.
patent: 6107623 (2000-08-01), Bateman et al.
patent: 6124137 (2000-09-01), Hutchens et al.
patent: 6127134 (2000-10-01), Minden et al.
patent: 6204500 (2001-03-01), Whitehouse et al.
patent: 6268144 (2001-07-01), Koster
patent: 6379970 (2002-04-01), Liebler et al.
patent: 2002/0045194 (2002-04-01), Cravatt et al.
patent: 2002/0076739 (2002-06-01), Aebersold et al.
patent: 2002/0150961 (2002-10-01), Bogyo et al.
patent: 2003/0003465 (2003-01-01), Little et al.
patent: WO 91/15228 (1991-10-01), None
patent: WO 00/11208 (2000-03-01), None
patent: WO 01/77668 (2001-10-01), None
patent: WO 01/77684 (2001-10-01), None
Adam et al., “Profiling the specific reactivity of the proteome with non-directed activity-based probes,” Chemistry & Biology 2000, 57:1-16, Jan. 2000.
Bergseid et al., “Small molecule-based chemical affinity system for the purification of proteins,” BioTechniques, 29:1126-1133, Nov. 2000.
Bogyo et al., “Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs,” Chemistry & Biology 2000, 7:27-38, Dec. 15, 1999.
Clauser et al., “Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE,” Proc.Natl.Acad.Sci.USA, 92:5072-5076, May 1995.
Cravatt and Sorensen, “Chemical strategies for the global analysis of protein function,” Current Opinion in Chemical Biology, 4: 663-668, 2000.
Cull and McHenry, “Preparation of extracts from prokaryotes,”Methods in Enzymology, vol. 182, 147-238,. 1990 edition.
Daniel et al., “FastTag™ nucleic acid labeling system . . . ,” BioTechniques, 24: 484-489, Mar. 1998.
U.S. Appl. No. 10/035,451, Bogyo et al.
DeLeenheer and Thienpont, “Applications of isotope dilution-mass spectrometry in clinical chemistry, pharma-cokinetics, and toxicology,” Mass Spectrometry Reviews, 11:249-307, 1992.
Eng et al., “An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database,” J.Am.Soc.Mass.Spectrometry, 5:976-989, 1994.
Greenbaum et al., “Epoxide electrophiles as activity-dependent profiling and discovery tools,” Chemistry & Biology 2000, 7:569-581, Aug. 1, 2000.
Gygl et al, “Protein analysis by mass spectrometry and sequence database searching: tools for cancer research in the post-genomic era,” Electrophoresis, 20: 310-319, 1999.
Gygl et al., “Correlation between protein and mRNA abundance in yeast,” Molecular and Cellular Biology, 19: 1720-1730, 1999.
Gygl et al., “Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology,” Proc. Nat.Acad.Sci.USA, 97:9390-9395, 2000.
Kasicka, “Recent advances in capillary electrophoresis of peptides,” Electrophoresis, 22:4139-4162, 2001.
Kidd et al, “Profiling serine hydrolase activities in complex proteomes,” Biochemistry, 40:4005-4015, 2001.
Laemmli, “Cleavage of structural proteins during the assembly of the head of bacteriophage T4,” Nature, 227: 680-685, 1970.
Link et al., “Identifying the major proteone components of haemophilus influenzae type-strain NCTC 8143,” Electrophoresis, 18: 1314-1334, 1997.
Liu et al., “Activity-based protein profiling: The Serine hydrolases,” Proc. Nat. Acad. Sci 1999, 96: 14694-14699, Dec. 21, 1999.
Mann and Wilm, “Error-tolerant identification of peptides in sequence databases by peptide sequence tags,” Anal. Chem., 66: 4390-4399, 1994.
Merchant and Weinberger, “Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry,” Electrophoresis, 21: 1164-1167, 2000.
Opiteck et al., “Comprehensive two-dimensional high-performance liquid chromatography for the isolation of Overexpressed proteins and proteome mapping,” Analytical Biochemistry, 258: 349-361, 1998.
Porco, “Organic synthesis using chemical tags: The “third leg” of parallel synthesis,” Combinatorial Chemistry & High Throughput Screening, 3: 93-102, 2000.
Sanchez and Smith, “Capillary electrophoresis,” Methods in Enzymology, 289:469-478, 1997.
Wright et al., “Proteinchip® surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel Protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures,” Prostate Cancer and Prostatic Diseases, 2: 264-276, 1999.
Xu, “Capillary electrophoresis,” Analytical Chemistry, 67: 463R-473R, 1995.
Mills et al., “Identification of a ligand binding site in the human neutrophil formyl peptide receptor using a site-specific fluorescent photoaffinity label and mass spectrometry.” The Journal of Biological Chemistry, 273(17): 10428-10435, 1998.
Supplementary European Search Report dated Dec. 13, 2004 for European Patent Application No. 02723286.7-2404-PCT/US0206234.
Activx Biosciences, Inc.
Counts Gary W.
Foley & Lardner
Le Long V.
Reiter Stephen E.
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