Protein silencing with Phylomers: A new tool for target validation and generating lead biologicals targeting protein interactions

Expert Opinion on Drug Discovery

Volumn 1, Issue 5, 2006, Pages 491-502

  Watt, Paul M ^a   Heinrich, Tatjana K ^b   Thomas, Wayne R ^b  

^a Phylogica Ltd   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

aptamer; functional proteomics; intrabodies; peptide; Phylomer; protein interaction; protein silencing; siRNA; target validation

Indexed keywords

EID: 77953376403     PISSN: 17460441     EISSN: 1746045X     Source Type: Journal    
DOI: 10.1517/17460441.1.5.491     Document Type: Review

References (84)

1. PRITCHARD JF, JURIMA-ROMET M, REIMER ML, MORTIMER E, ROLFE B, CAYEN MN: Making better drugs: decision gates in non-clinical drug development. Nat. Rev. Drug Discov. (2003) 2:542-553.
2. BLEICHER KH, BOHM HJ, MULLER K, ALANINE AI: Hit and lead generation: beyond high-throughput screening. Nat. Rev. Drug Discov. (2003) 2:369-378.
3. XING Y, RESCH A, LEE C: The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res. (2004) 14:426-441.
4. SPITZER M, LORKOWSKI S, CULLEN P, SCZYRBA A, FUELLEN G: IsoSVM-distinguishing isoforms and paralogs on the protein level. BMC Bioinformatics (2006) 7:110.
5. LANDER E, LINTON L, BIRREN B et al.: Initial sequencing and analysis of the human genome. Nature (2001) 409:860-921.
6. VENTER J, ADAMS M, MYERS E et al.: The sequence of the human genome. Science (2001) 291:1304-1351.
7. PAPATHANASIOU P, GOODNOW CC: ENU mouse mutagenesis: gene combinations specifying the immune system. Annu. Rev. Genet. (2005) 39:241-262.
8. NEIMS K, GOODNOW CC: Genome-wide mutagenesis with ENU to discover immune regulators. Immunity (2001) 15:409-419.
9. DREWS J: Drug discovery: a historical perspective. Science (2000) 287:1960-1964.
10. MOFFAT J, SABATINI D: Building mammalian signalling pathways with RNAi screens. Nat. Rev. Mol. Cell Biol. (2006) 7:177-187.
11. TISCORNIA G, SINGER O, IKAWA M, VERMA I: A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl. Acad. Sci. USA (2003) 100:1844-1848.
12. GAVIN AC, ALOY P, GRANDI P et al.: Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 440:631-636.
13. GE H, WALHOUT, VIDAL M: Integrating omic information: a bridge between genomics and systems biology. Trends Genet. (2003) 19:551-559.
14. RUAL JF, VENKATESAN K, HAO T et al.: Towards a proteome-scale map of the human protein-protein interaction network. Nature (2005) 437:1173-1178.
15. DAMBROSIO C, ARENA S, FULCOLI G et al.: Hyperphosphorylation of JNK-interacting protein 1, a protein associated with Alzheimers disease. Mol. Cell. Proteomics (2006) 5:97-113.
16. STROSBERG AD: Protein interaction mapping for target validation: the need for an integrated combinatory process involving complementary approaches. Curr. Opin. Mol. Ther. (2002) 4:594-600.
17. WARNER G, ADELEYE Y, IDEKER T: Interactome networks: the state of the science. Genome Biol. (2006) 7:301.
18. WATT P: Screening for peptide drugs from the natural repertoire of biodiverse protein folds. Nat. Biotechnol. (2006) 24:177-183.
19. ARCHAKOV A, GOVORUN V, DUBANOV A et al.: Protein-protein interactions as a target for drugs in proteomics. Proteomics (2003) 3:380-391.
20. GOLEMIS EA, TEW KD, DADKE D: Protein interaction-targeted drug discovery: evaluating critical issues. Biotechniques (2002) 32:636-638.
21. FISCHER P, LANE DP: Small-molecule inhibitors of the p53 suppressor HDM2: have protein-protein interactions come of age as drug targets? Trends Pharmacol. Sci. (2004) 25:344-346.
22. PAVLOU A, REICHERRT J: Recombinant protein therapeutics: success rates, values and market trends to 2010. Nat. Biotechnol. (2004) 22:1513-1519.
23. WILLIAMS BR, ZHU Z: Intrabody-based approaches to cancer therapy: status and prospects. Curr. Med. Chem. (2006) 13:1473-1480.
24. STOCKS M: Intrabodies as drug discovery tools and therapeutics. Curr. Opin. Chem. Biol. (2005) 9:359-365.
25. HOLT LJ, HERRING C, JESPERS LS, WOOLVEN BP, TOMLINSON IM: Domain antibodies: proteins for therapy. Trends Biotechnol. (2003) 21:484-490.
26. REVETS H, DE BAETSELIER P, MUYLDERMANS S: Nanobodies as novel agents for cancer therapy. Expert Opin. Biol. Ther. (2005) 5:111-124.
27. CATTANEO A, BIOCCA S: The selection of intracellular antibodies. EMBO J. (1999) 22:1025-1035.
28. TSE E, LOBATO M, FORSTER A, TNAKA T, CHUNG T, RABBITTS T: Intracellular antibody capture technology: application to selection of single chain Fv recognising the BCR-ABL oncogenic protein. J. Mol. Biol. (2002) 317:85-94.
29. TANAKA T, RABBITTS T: Intrabodies based on intracellular capture frameworks that bind the RAS protein with high affinity and impair oncogenic transformation. EMBO J. (2003) 22:1025-1035.
30. CHEN Y, SHEN Y, GUO X et al.: Transdermal protein delivery by a coadministered peptide identified by phage display. Nat. Biotechnol. (2006) 24:455-460.
31. LIU S, LU H, NIU J, XU Y, WU S, JIANG S: Different from the HIV fusion inhibitor C34, the anti-HIV drug Fuzeon (T-20) inhibits HIV1 entry by targeting multiple sites in gp41 and gp120. J. Biol. Chem. (2005) 280:11259-11273.
32. MATTHEWS T, SALGO M, GREENBERG M, CHUNG J, DEMASI R, BOLOGNESI D: Enfuvirtide: the first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nat. Rev. Drug Discov. (2004) 3:215-255.
33. WAGSTAFF K, JANS D: Protein transduction: cell penetrating peptides and their therapeutic applications. Curr. Med. Chem. (2006) 13:1371-1387.
34. WADIA J, DOWDY S: Protein transduction technology. Curr. Opin. Biotechnol. (2002) 13:52-56.
35. ZHAO M, WEISSLEDER R: Intracellular cargo delivery using TAT peptide and derivatives. Med. Res. Rev. (2004) 24:1-12.
36. WENDER P, MITCHELL D, PATTABIRAMAN K, PELKEY E, STEINMAN L, ROTHBARD J: The design, synthesis, and evaluation of molecules that enable or enhance cellular uptake: peptoid molecular transporters. Proc. Natl. Acad. Sci. USA (2000) 97:13003-13008.
37. TEMSAMANI J, VIDAL P: The use of cell-penetrating peptides for drug delivery. Drug Discov. Today (2004) 9:1012-1018.
38. OEHLKE J, SCHELLER A, WIESNER B, KRAUSE E, BEYERMANN M: Cellular uptake of an alpha-helical amphipathic model peptide with the potential to deliver polar compounds into the cell interior non-endocytically. Biochim. Biophys. Acta (1998) 1414:127-139.
39. RESHETNYAK Y, ANREEV O, LEHNERT U, ENGELMAN D: Translocation of molecules into cells by pH-dependent insertion of a transmembrane helix. Proc. Natl. Acad. Sci. USA (2006) 103:6460-6465.
40. DASGUPTA P, SUN J, WANG S et al.: Disruption of the Rb-Raf-1 interaction inhibits tumor growth and angiogenesis. Mol. Cell. Biol. (2004) 24:9527-9541.
41. MAROUN RG, GAYET S, BENLEULMI MS et al.: Peptide inhibitors of HIV-1 integrase dissociate the enzyme oligomers. Biochemistry (2001) 40:13840-13848.
42. ZHAO L, OREILLY MK, SHULTZ MD, CHMIELEWSKI J: Interfacial peptide inhibitors of HIV-1 integrase activity and dimerization. Bioorg. Med. Chem. Lett. (2003) 13:1175-1177.
43. BARR RK, HOPKINS RM, WATT PM, BOGOYEVITCH MA: Reverse two-hybrid screening identifies residues of JNK required for interaction with the kinase interaction motif of JNK-interacting protein-1. J. Biol. Chem. (2004) 279:43178-43189.
44. BARR RK, BOEHM I, ATTWOOD PV, WATT PM, BOGOYEVITCH MA: The critical features and the mechanism of inhibition of a kinase interaction motif-based peptide inhibitor of JNK. J. Biol. Chem. (2004) 279:36327-36338.
45. KANETO H, NAKATANI Y, MIYATSUKA T et al.: Possible novel therapy for diabetes with cell-permeable JNK-inhibitory peptide. Nat. Med. (2004) 10:1128-1132.
46. MORFINI G, PIGINO G, SZEBENYI G, YOU Y, POLLEMA S, BRADY S: JNK mediates pathogenic effects of polyglutamine-expanded androgen receptor on fast axonal transport. Nat. Neurosci. (2006) 9:907-916.
47. BORSELLO T, CLARKE PG, HIRT L et al.: A peptide inhibitor of c-Jun N-terminal kinase protects against excitotoxicity and cerebral ischemia. Nat. Med. (2003) 9:1180-1186.
48. CHAN B, GREENAN G, MCKEON F, ELLENBERGER T: Identification of a peptide fragment of DSCR1 that competitively inhibits calcineurin activity in vitro and in vivo. Proc. Natl. Acad. Sci. USA (2005) 102:13075-13080.
49. STOCKTON RA, SCHAEFER E, SCHWARTZ MA: p21-Activated kinase regulates endothelial permeability through modulation of contractility. J. Biol. Chem. (2004) 279:46621-46630.
50. KIOSSES WB, HOOD J, YANG S et al.: A dominant-negative p65 PAK peptide inhibits angiogenesis. Circ. Res. (2002) 90:697-702.
51. ADLER M, SETO MH, NITECKI D, LIN J-H, LIGHT DR, MORSER J: The structure of a 19-residue fragment from the C-loop of the fourth epidermal growth factor-like domain of thrombomodulin. J. Biol. Chem. (1995) 270:23366-23372.
52. VRANKEN WF, JAMES S, BENNETT HP, NI F: Solution structures of a 30-residue amino-terminal domain of the carp granulin-1 protein and its amino-terminally truncated 3-30 subfragment: implications for the conformational stability of the stack of two hairpins. Proteins (2002) 47:14-24.
53. MATTHEWS L, DAVIS R, SMITH G: Immunogenetically fit subunit vaccine components via epitope discovery from natural peptide libraries. J. Immunol. (2002) 169:837-846.
54. WOLF Y, GRISHIN N, KOONIN E: Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. (2000) 299:897-905.
55. ORENGO C, MICHIE A, JONES S, SWINDELLS M, THORNTON J: CATH - a hierarchic classification of protein domain structures. Structure (1997) 5:1093.
56. HARRISON H, PEARL F, SILLITOE I, SLIDEL T, MOTT R, THORNTON J, ORENGO C: Recognising the fold of a protein structure. Bioinformatics (2003) 19:1748-1759.
57. COULSON A, MOULT J: A unifold mesofold and superfold model of protein fold use. Proteins (2002) 46:61-71.
58. ORENGO CA, THORNTON JM: Protein families and their evolution - a structural perspective. Annu. Rev. Biochem. (2005) 74:867-900.
59. ABELN S, DEANE CM: Fold usage on genomes and protein fold evolution. Proteins (2005) 60:690-700.
60. PHILLIPS SE: Built by association: structure and function of helix-loop-helix DNA-binding proteins. Structure (1994) 2:1-4.
61. VINSON C, ACHARYA A, TAPAROWSKY EJ: Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta (2006) 1759:4-12.
62. MATTHEWS JM, SUNDE M: Zinc fingers-folds for many occasions. IUBMB Life (2002) 54:351-355.
63. KOCH M, WALDMANN H: Protein structure similarity clustering and natural product structure as guiding principles in drug discovery. Drug Discov. Today (2005) 10:471-483.
64. SERVICE R: Structural genomics, round 2. Science (2005) 307:1554-1557.
65. YANG AS, HONIG B: An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol. (2000) 301:691-711.
66. MOREAU V, GRANIER C, VILLARD S, LAUNE D, MOLINA F: Discontinuous epitope prediction based on mimotope analysis. Bioinformatics (2006) 22:1088-1095.
67. VAN REGENMORTEL M: From absolute to exquisite specificity. Reflections on the fuzzy nature of species, specificity and antigenic sites. J. Immunol. Methods (1998) 216:37-48.
68. PARISSI V, CALMELS C, DE SOULTRAIT VR et al.: Functional interactions of human immunodeficiency virus type 1 integrase with human and yeast HSP60. J. Virol. (2001) 75:11344-11353.
69. DE SOULTRAIT V, CAUMONT A, PARISSI V et al.: A novel short peptide is a specific inhibitor of human immunodeficiency virus type 1 integrase. J. Mol. Biol. (2002) 318:45-58.
70. CAPONIGRO G, ABEDI MR, HURLBURT AP, MAXFIELD A, JUDDW, KAMB A: Transdominant genetic analysis of a growth control pathway. Proc. Natl. Acad. Sci. USA (1998) 95:7508-7513.
71. GUDKOV AV, KAZAROV AR, THIMMAPAYA R, AXENOVICH SA, MAZO IA, RONINSON IB: Cloning mammalian genes by expression selection of genetic suppressor elements: association of kinesin with drug resistance and cell immortalization. Proc. Natl. Acad. Sci. USA (1994) 91:3744-3748.
72. PARK S, RAINES R: Genetic selection for dissociative inhibitors of designated protein/protein interactions. Nat. Biotechnol. (2000) 18:847-851.
73. COLAS P, COHEN B, JESSEN T, GRISHINA I, MCCOY J, BRENT R: Genetic selection of peptide aptamers that recognize and inhibit cuclin-dependent kinase 2. Nature (1996) 380:548-550.
74. LADNER RC: Constrained peptides as binding entities. Trends Biotechnol. (1995) 13:426-430.
75. XU C, LUO Z: Inactivation of Ras function by allele specific peptide apatamers. Oncogene (2002) 21:5753-5757.
76. CRAWFORD M, WOODMAN R, KO FERRRIGNO P: Peptide aptamers: tools for biology and drug discovery. Brief. Funct. Genomic. Proteomic. (2003) 2:72-79.
77. BUTZ K, DENK C, ULLMANN A, SCHEFFNER M, HOPPE-SEYLER F: Induction of apoptosis in human papillomavirus-positive cancer cells by peptide aptamers targeting the viral E6 oncoprotein. Proc. Natl. Acad. Sci. USA (2000) 97:6693-6697.
78. BINZ H, AMSTUTZ P, PLUCKTHUN A: Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. (2005) 23:1257-1268.
79. LADNER RC, SATO AK, GORZELANY J, DE SOUZA M: Phage display-derived peptides as therapeutic alternatives to antibodies. Drug Discov. Today (2004) 9:525-529.
80. SZYMKOWSKI D: Creating the next generation of protein therapeutics through rational drug design. Curr. Opin. Drug Discov. Dev. (2005) 8:590-600.
81. COLAS P, COHEN B, KO FERRRIGNO P, SILVER P, BRENT R: Targeted modification and transportation of cellular proteins. Proc. Natl. Acad. Sci. USA (2000) 97:13720-13725.
82. ZHOU P, BOGACKI R, MCREYNOLDS L, HOWLEY P: Harnessing the ubiquitination machinery to target the degradation of specific cellular proteins. Mol. Cell (2000) 6:751-756.
83. LUEKING A, CAHILL D, MULLNER S: Protein biochips: a new and versatile platform technology for molecular medicine. Drug Discov. Today (2005) 10:789-794.
84. http://www.prolexys.com Prolexys Pharmaceuticals company website. (2006).