Rational drug design via intrinsically disordered protein

Trends in Biotechnology

Volumn 24, Issue 10, 2006, Pages 435-442

  Cheng, Yugong ^a   LeGall, Tanguy ^a   Oldfield, Christopher J ^a   Mueller, James P ^a   Van, Ya Yue J ^a   Romero, Pedro ^a   Cortese, Marc S ^a   Uversky, Vladimir N ^a   Dunker, A Keith ^a  

^a Molecular Kinetics Inc 6201 La Pas Trail   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COUPLED BINDING; DRUG DISCOVERY RATES; PROTEIN-PROTEIN INTERACTIONS;

MOLECULAR DYNAMICS; PROTEINS;

DRUG PRODUCTS;

AMINO ACID; NEW DRUG; NUCLEOTIDE; PROTEIN; PROTEIN MDM2; PROTEIN P53;

AMINO ACID SEQUENCE; ARTICLE; CONSENSUS SEQUENCE; DATA ANALYSIS SOFTWARE; DISORDER BASED RATIONAL DRUG DESIGN; DRUG DESIGN; DRUG PROTEIN BINDING; DRUG RESEARCH; FOOD AND DRUG ADMINISTRATION; GENOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

CHEMISTRY, PHARMACEUTICAL; DRUG DESIGN; HUMANS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; STRUCTURE-ACTIVITY RELATIONSHIP; TUMOR SUPPRESSOR PROTEIN P53;

EID: 33748272622     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2006.07.005     Document Type: Article

References (53)

1. Drews J., and Ryser S. The role of innovation in drug development. Nat. Biotechnol. 15 (1997) 1318-1319
2. Drews J. Drug discovery: a historical perspective. Science 287 (2000) 1960-1964
3. Estrada E. Virtual identification of essential proteins within the protein interaction network of yeast. Proteomics 6 (2006) 35-40
4. Jones R.B., et al. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439 (2006) 168-174
5. Cochran A.G. Antagonists of protein-protein interactions. Chem. Biol. 7 (2000) R85-R94
6. Arkin M. Protein-protein interactions and cancer: small molecules going in for the kill. Curr. Opin. Chem. Biol. 9 (2005) 317-324
7. Fry D.C., and Vassilev L.T. Targeting protein-protein interactions for cancer therapy. J. Mol. Med. 83 (2005) 955-963
8. Arkin M.R., and Wells J.A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat. Rev. Drug Discov. 3 (2004) 301-317
9. Koshland Jr. D.E., et al. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5 (1966) 365-385
10. Chene P. Inhibition of the p53-MDM2 interaction: targeting a protein-protein interface. Mol. Cancer Res. 2 (2004) 20-28
11. Vassilev L.T., et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303 (2004) 844-848
12. Anderson C.W., and Appella E. Signalling to the p53 tumour suppressor through pathways activated by genotoxic and nongenotoxic stress. In: Bradshaw R.A., and Dennis E.A. (Eds). Handbook of Cell Signalling (2004), Academic Press 237-247
13. Wasylyk C., et al. p53-mediated death of cells overexpressing MDM2 by an inhibitor of MDM2 interaction with p53. Oncogene 18 (1999) 1921-1934
14. Kussie P.H., et al. Structure of the MDM2 oncoprotein bound to the p53 tumour suppressor transactivation domain. Science 274 (1996) 948-953
15. Chene P. A small synthetic peptide, which inhibits the p53-hmd2 interaction, stimulates the p53 pathway in tumour cell lines. J. Mol. Biol. 299 (2000) 245-253
16. Bottger A., et al. Design of a synthetic Mdm2-binding mini protein that activates the p53 response in vivo. Curr. Biol. 7 (1997) 860-869
17. Vassilev L.T. Small-molecule antagonists of p53-MDM2 binding - research tools and potential therapeutics. Cell Cycle 3 (2004) 419-421
18. Obradovic Z., et al. Predicting intrinsic disorder from amino acid sequence. Proteins 53 Suppl. 6 (2003) 566-572
19. Dunker A.K., et al. Intrinsic disorder and protein function. Biochemistry 41 (2002) 6573-6582
20. Dunker A.K., et al. Identification and functions of usefully disordered proteins. Adv. Protein Chem. 62 (2002) 25-49
21. Kissinger C.R., et al. Crystal structures of human calcineurin and the human Fkbp12-Fk506-calcineurin complex. Nature 378 (1995) 641-644
22. + binding to alpha-synuclein regulates ligand binding and oligomerization. J. Biol. Chem. 276 (2001) 22680-22684
23. Yamamoto K., et al. BCL-2 is phosphorylated and inactivated by an ASK1/Jun N-terminal protein kinase pathway normally activated at G(2)/M. Mol. Cell. Biol. 19 (1999) 8469-8478
24. Brown H.G., and Hoh J.H. Entropic exclusion by neurofilament sidearms: a mechanism for maintaining interfilament spacing. Biochemistry 36 (1997) 15035-15040
25. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 27 (2002) 527-533
26. Tompa P., and Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J. 18 (2004) 1169-1175
27. Jin Y., and Dunbrack Jr. R.L. Assessment of disorder predictions in CASP6. Proteins 61 (2005) 167-175
28. Romero P., et al. Sequence complexity of disordered protein. Proteins 42 (2001) 38-48
29. Obradovic Z., et al. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins 61 Suppl. 7 (2005) 176-182
30. Peng K., et al. Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. Comput. Biol. 3 (2005) 35-60
31. Uversky V.N., et al. Why are "natively unfolded" proteins unstructured under physiologic conditions?. Proteins 41 (2000) 415-427
32. Iakoucheva L.M., et al. Intrinsic disorder in cell-signalling and cancer-associated proteins. J. Mol. Biol. 323 (2002) 573-584
33. Dunker A.K., et al. Intrinsic protein disorder in complete genomes. Genome Informatics Series: Proceedings of the Workshop on Genome Informatics 11 (2000) 161-171
34. Ward J.J., et al. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol. 337 (2004) 635-645
35. Oldfield C.J., et al. Comparing and combining predictors of mostly disordered proteins. Biochemistry 44 (2005) 1989-2000
36. Liu J., and Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10 (2001) 1970-1979
37. Carl P.L., et al. Most nuclear systemic autoantigens are extremely disordered proteins: implications for the etiology of systemic autoimmunity. Arthritis Res. Ther. 7 (2005) R1360-R1374
38. Puntervoll P., et al. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 31 (2003) 3625-3630
39. Iakoucheva L.M., et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 32 (2004) 1037-1049
40. Diella F., et al. Phospho. ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5 (2004) 79
41. Dyson H.J., and Wright P.E. Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol. 6 (2005) 197-208
42. Schulz G.E. Nucleotide binding proteins. In: Balaban M. (Ed). Molecular Mechanism of Biological Recognition (1979), Elsevier 79-94
43. Issaeva N., et al. Rescue of mutants of the tumour suppressor p53 in cancer cells by a designed peptide. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 13303-13307
44. Garner E., et al. Predicting disordered regions from amino acid sequence: common themes despite differing structural characterization. Genome Inform. Ser. Workshop Genome Inform. 9 (1998) 201-213
45. Fuxreiter M., et al. Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J. Mol. Biol. 338 (2004) 1015-1026
46. Oldfield C.J., et al. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry 44 (2005) 12454-12470
47. Callebaut I., et al. Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell. Mol. Life Sci. 53 (1997) 621-645
48. Lee H., et al. Local structural elements in the mostly unstructured transcriptional activation domain of human p53. J. Biol. Chem. 275 (2000) 29426-29432
49. Callaghan A.J., et al. Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. J. Mol. Biol. 340 (2004) 965-979
50. Kingston R.L., et al. Structural basis for the attachment of a paramyxoviral polymerase to its template. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 8301-8306
51. Bourhis J.M., et al. The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partner. Virus Res. 99 (2004) 157-167
52. Houston Jr. M.E., et al. Lactam bridge stabilization of alpha-helical peptides: ring size, orientation and positional effects. J. Pept. Sci. 1 (1995) 274-282
53. Matsui H., et al. Protein therapy: in vivo protein transduction by polyarginine (11R) PTD and subcellular targeting delivery. Curr. Protein Pept. Sci. 4 (2003) 151-157