Target validation and drug discovery using genomic and protein-protein interaction technologies

Expert Opinion on Therapeutic Targets

Volumn 6, Issue 4, 2002, Pages 517-531

  Pillutla, Renuka C ^a   Fisher, Paul B ^a   Blume, Arthur J ^a   Goldstein, Neil I ^a  

^a DGI BioTechnologies   (United States)

Author keywords

Biological interactions; Functional genomics; In vitro display; Interaction mapping; Phage display; Phenogenix ; Protein protein interactions; Proteome Panning ; Proteomics; RaSH; RSDD; Target identification; Target validation; Yeast two hybrid

Indexed keywords

CALMODULIN BINDING PROTEIN; CETUXIMAB; DNA BINDING PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR; ERYTHROPOIETIN; MONOCLONAL ANTIBODY; ONCOPROTEIN; PACLITAXEL; PROTEOME; RNA BINDING PROTEIN; TRASTUZUMAB;

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DRUG TARGETING; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENE TECHNOLOGY; HUMAN; HUMAN CELL; HUMAN GENOME; HYBRIDIZATION; NONHUMAN; PHAGE DISPLAY; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TWO HYBRID SYSTEM; VALIDATION PROCESS;

ANIMALS; CELLS, CULTURED; CLONING, MOLECULAR; COMBINATORIAL CHEMISTRY TECHNIQUES; DNA, COMPLEMENTARY; DRUG DELIVERY SYSTEMS; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOMICS; HELA CELLS; HUMANS; MAMMALS; NUCLEIC ACID HYBRIDIZATION; PEPTIDE LIBRARY; POLYMERASE CHAIN REACTION; PROTEIN INTERACTION MAPPING; PROTEOMICS; SUBTRACTION TECHNIQUE; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 0036045366     PISSN: 14728222     EISSN: None     Source Type: Journal    
DOI: 10.1517/14728222.6.4.517     Document Type: Article

References (108)

1. Drug discovery: A historical perspective
2. The sequence of the human genome
3. Initial sequencing and analysis of the human genome
4. A draft annotation and overview of the human genome
5. A hierarchical approach to protein molecular evolution
6. Novel folded protein domains generated by combinatorial shuffling of polypeptide segments
7. Recent developments in computational proteomics
8. The promise of structural genomics in the discovery of new antimicrobial agents
9. Structural genomics: Bridging functional genomics and structure-based drug design
10. Domain combinations in archeal, eubacterial and eukaryotic proteomes
11. Domain repertoires as a tool to derive protein recognition rules
12. Quantitative monitoring of gene expression patterns with a complementary DNA microarray
13. Identification and temporal expression pattern of genes modulated during irreversible growth arrest and terminal differentiation in human melanoma cells
14. Microarrays: Biotechnology's discovery platform for functional genomics
15. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction
16. Identification of the human prostatic carcinoma oncogene PTI-1 by rapid expression cloning and differential RNA display
17. Reciprocal subtraction differential RNA display: An efficient and rapid procedure for isolating differentially expressed gene sequences
18. RSDD-Reciprocal substraction differential RNA display
19. Serial analysis of gene expression
20. Gene expression profiles in normal and cancer cells
21. Use of a sensitive and efficient subtraction hybridization protocol for the identification of genes differentially regulated during the induction of differentiation in human melanoma cells
22. Substraction hybridization identifies a novel melanoma differentiation associated gene, mda-7, modulated during human melanoma differentiation, growth and progression
23. Subtractive cloning: Past, present and future
24. Substraction hybridization identifies a progression elevated gene PEG-3 with sequence homology to a growth arrest and DNA damage inducible gene
25. Subtractive hybridization-genetic takeaways and the search for meaning
26. Identification of human renal cell carcinoma associated genes by suppression subtractive hybridization
27. RaSH, a rapid substraction hybridization approach for identifying and cloning differentially expressed genes
28. Comparative genomic analysis of tumours: Detection of DNA lossess and amplification
29. Identifying differences in mRNA expression by representational difference analysis of cDNA
30. Cloning of differentially expressed genes in an HIV-1 resistant T cell clone by rapid subtraction hybridization, RaSH
31. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays
32. Gene expression microarray analysis in cancer biology, pharmacology and drug development: Progress and potential (2)
33. Genomic profiling of short-and long-term caloric restriction effects in the liver of ageing mice
34. Identification of tumour markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray
35. Towards a novel classification of human malignancies based on gene expression patterns
36. Molecular markers and determinants of human prostate cancer metastasis
37. Cooperation between AP1 and PEA3 sites within the progression elevated gene-3 (PEG-3) promoter regulate basal and differential expression of PEG-3 during progression of the oncogenic phenotype in transformed rat embryo cells
38. PEA3 sites within the progression elevated gene-3 (PEG-3) promoter and mitogen activated protein kinase contribute to differential PEG-3 expression in Ha-ras and v-raf oncogene transformed rat embryo fibroblast cells
39. Development of a facile method for high-throughput screening with reporter gene assays
40. RepGene: A spreadsheet template for the management of reporter gene assays
41. In vitro high throughput screening of compounds for favorable metabolic properties in drug discovery
42. RaSH-Rapid subtraction hybridization
43. Cloning and characterization of human ubiquitin-processing protease-43 from terminally differentiated human melanoma cells using a rapid subtraction hybridization protocol RaSH
44. Different strategies of differentiation display: Areas of application
45. Differential display of mRNA
46. Recent advances in differential display
47. Cloning differentially expressed mRNAs
48. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries
49. Identification and cloning of human astrocyte genes displaying elevated expression after infection with HIV-1 or exposure to HIV-1 envelope glycoprotein by rapid subtraction hybridization, RaSH
50. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
51. Proteomics. Integrating interactomes
52. A motif-based profile scanning approach for genome-wide prediction of signalling pathways
53. Functional organization of the yeast proteome by systematic analysis of protein complexes
54. A generic protein purification method for protein complex characterization and proteome exploration
55. Printing proteins as microarrays for high-throughput function determination
56. Global analysis of protein activities using proteome chips
57. A novel genetic system to detect protein-protein interactions
58. The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest
59. The two-hybrid system: An assay for protein-protein interactions
60. Applications of interaction traps/two-hybrid systems to biotechnology research
61. High-throughput yeast two-hybrid assays for large-scale protein interaction mapping
62. Cdi1, a human G1 and S phase protein phosphatase that associates with CDK2
63. Mammalian Ras interacts directly with the serine/threonine kinase Raf
64. The retinoblastoma protein associates with the protein phosphatase Type I catalytic subunit
65. The p21 Cdk-interacting protein Cip 1 is a potent inhibitor of G1 cyclin-dependent kinases
66. Fused protein domains inhibit DNA binding by Lex A
67. Negative effect of the transcriptional activator GAL4
68. Selective inhibition of activated but not basal transcription by the acidic activation domain of VP16: Evidence for transcriptional adaptors
69. Transcriptional transactivation by selected short random peptides attached to lexA-GFP fusion proteins
70. A three-hybrid system to detect RNA-protein interactions in vivo
71. Using the three-hybrid system to detect and analyse RNA-protein interactions
72. The genes for histone RNA hairpin binding protein is located on chromosome-4 and encodes a novel type of RNA binding protein
73. The protein that binds the 3' end of histone mRNA: A novel RNA-binding protein required for histone premRNA processing
74. A conserved RNA-binding protein that regulates sexual fates in the C. Elegans hermaphrodite germ line
75. The star protein GLD-1 is a translational regulator of sexual identity in C. elegans
76. Two Xenopus proteins that bind the 3′ end of histone mRNA for translational control of protein synthesis during oogenesis
77. Regulation of eukaryotic protein synthesis: Selective influenza viral mRNA translation is mediated by cellular RNA binding protein
78. Smaug, a novel RNA-binding protein that operate a translational switch in Drosophila
79. Stress-induced nuclear bodies are sites of accumulation of premRNA processing factors
80. Molecular cloning of the olfactory neuronal transcriptional factor Olf-1 by genetic selection in yeast
81. Isolation of ORC6, a component of the yeast origin recognition complex by a one hybrid system
82. Isolation of a cDNA encoding a metal response element binding protein using a novel expression cloning procedure: The one hybrid system DNA
83. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions
84. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
85. A comprehensive two-hybrid analysis to explore the yeast protein interactome
86. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
87. The protein-protein interaction map of Helicobacter pylori
88. Protein interaction verification and functional annotation by integrated analysis of genome-scale data
89. Comparative assessment of large-scale data sets of protein-protein interactions
90. Genome organization: Teamed up for transcription
91. Dominant effector genetics in mammalian cells
92. Transdominant genetic analysis of a growth control system
93. Isolation of an AP-1 repressor by a novel method for detecting protein-protein interactions
94. A novel in vivo assay for the analysis of protein-protein interaction
95. Applications of display technology in protein analysis
96. Filamentous fusion phage cloning vectors for the study of epitopes and design of vaccines
97. Applications of combinatorial technologies to drug discovery. I. Background and peptide combinatorial libraries
98. Structural and mechanistic determinants of affinity and specificity of ligands discovered or engineered by phage display
99. Display of biologically active proteins on the surface of filamentous phages: A cDNA cloning system for selection of functional gene products linked to the genetic information responsible for their production
100. T7 phage display: A novel genetic selection system for cloning RNA-binding proteins from cDNA libraries
101. Mapping signal transduction pathways by phage display
102. RNA-peptide fusions for the in vitro selection of peptides and proteins
103. Isolation of high-affinity ligand-binding proteins by periplasmic expression with cytometric screening (PECS)
104. A combined experimental strategy to define protein interaction networks for peptide recognition modules
105. The use of peptides in Diogenesis®: A novel approach to drug discovery and phenomics
106. A surrogate-based approach for postgenomic partner identification
107. Identification of an allosteric binding site on the transcription factor p53 using a phage-displayed peptide library
108. Peptides identify the critical hotspots involved in the biological activation of the insulin receptor