Using peptides to study protein-protein interactions

Future Medicinal Chemistry

Volumn 2, Issue 6, 2010, Pages 989-1003

  Benyamini, Hadar ^a   Friedler, Assaf ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTIN; FLUORESCEIN; G PROTEIN COUPLED RECEPTOR; GLYCOPROTEIN GP 130; HYDROCARBON; INTERLEUKIN 6; PEPTIDE; PEPTIDOMIMETIC AGENT; PROTEIN INHIBITOR;

ACETYLATION; ANISOTROPY; CIRCULAR DICHROISM; CYCLIZATION; DRUG DESIGN; ENZYME LINKED IMMUNOSORBENT ASSAY; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNOASSAY; ISOTHERMAL TITRATION CALORIMETRY; KAPOSI SARCOMA; LEUKEMIA CELL; NUCLEAR MAGNETIC RESONANCE; OLIGOMERIZATION; PEPTIDE MAPPING; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEOMICS; REVIEW; SIGNAL TRANSDUCTION; SURFACE PLASMON RESONANCE; VIRUS REPLICATION; X RAY CRYSTALLOGRAPHY;

ANIMALS; HUMANS; MODELS, MOLECULAR; PEPTIDES; PROTEIN ARRAY ANALYSIS; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 77953639812     PISSN: 17568919     EISSN: None     Source Type: Journal    
DOI: 10.4155/fmc.10.196     Document Type: Review

References (99)

1. Cusick ME, Klitgord N, Vidal M, Hill DE. Interactome: gateway into systems biology. Hum. Mol. Genet. 14(2), R171-R181 (2005).
2. Vidal M. A unifying view of 21st century systems biology. FEBS Lett. 583(24), 3891-3894 (2009).
3. Fields S, Song O. A novel genetic system to detect protein-protein interactions. Nature 340(6230), 245-246 (1989).
4. Barrios-Rodiles M, Brown KR, Ozdamar B et al. High-throughput mapping of a dynamic signaling network in mammalian cells. Science 307(5715), 1621-1625 (2005).
5. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003).
6. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17(10), 1030-1032 (1999).
7. Bhardwaj N, Lu H. Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics 21(11), 2730-2738 (2005).
8. Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc. Natl Acad. Sci. USA 101(24), 9033-9038 (2004).
9. Lee LC, Hunter JJ, Mujeeb A, Turck C, Parslow TG. Evidence for a-helical conformation of an essential N-terminal region in the human Bcl2 protein. J. Biol. Chem. 271(38), 23284-23288 (1996).
10. Sattler M, Liang H, Nettesheim D et al. Structure of Bcl-XL-Bak peptide complex: recognition between regulators of apoptosis. Science 275(5302), 983-986 (1997).
11. Merrifield RB. Solid-phase peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc. 85(14), 2149-2154 (1963).
12. Kent SB. Total chemical synthesis of proteins. Chem. Soc. Rev. 38(2), 338-351 (2009).
13. Dawson PE, Kent SB. Synthesis of native proteins by chemical ligation. Annu. Rev. Biochem. 69, 923-960 (2000).
14. Kochendoerfer GG, Chen SY, Mao F et al. Design and chemical synthesis of a homogeneous polymer-modified erythropoiesis protein. Science 299(5608), 884-887 (2003).
15. Torbeev VY, Kent SB. Convergent chemical synthesis and crystal structure of a 203 amino acid 'covalent dimer' HIV-1 protease enzyme molecule. Angew Chem. Int. Ed. Engl. 46(10), 1667-1670 (2007).
16. Craik DJ. Chemistry. Seamless proteins tie up their loose ends. Science 311(5767), 1563-1564 (2006).
17. Craik DJ. Circling the enemy: cyclic proteins in plant defence. Trends Plant Sci. 14(6), 328-335 (2009).
18. Daly NL, Rosengren KJ, Craik DJ. Discovery, structure and biological activities of cyclotides. Adv. Drug Deliv. Rev. 61(11), 918-930 (2009).
19. Davies JS. The cyclization of peptides and depsipeptides. J. Pept. Sci. 9(8), 471-501 (2003).
20. Lambert J, Mitchell J, Roberts K. The synthesis of cyclic peptides. J. Chem. Soc. Perkin Trans. 1, 471-484 (2001).
21. Byk G, Halle D, Zeltser I, Bitan G, Selinger Z, Gilon C. Synthesis and biological activity of nk-1 selective, N-backbone cyclic analogs of the C-terminal hexapeptide of substance P. J. Med. Chem. 39(16), 3174-3178 (1996).
22. Chatterjee J, Gilon C, Hoffman A, Kessler H. N-methylation of peptides: a new perspective in medicinal chemistry. Acc. Chem. Res. 41(10), 1331-1342 (2008).
23. Chatterjee J, Ovadia O, Gilon C, Hoffman A, Mierke D, Kessler H. N-methylated cyclic pentapeptides as template structures. Adv. Exp. Med. Biol. 611, 109-110 (2009).
24. Friedler A, Friedler D, Luedtke NW, Tor Y, Loyter A, Gilon C. Development of a functional backbone cyclic mimetic of the HIV-1 Tat arginine-rich motif. J. Biol. Chem. 275(31), 23783-23789 (2000).
25. Friedler A, Zakai N, Karni O et al. Backbone cyclic peptide, which mimics the nuclear localization signal of human immunodeficiency virus type 1 matrix protein, inhibits nuclear import and virus production in nondividing cells. Biochemistry 37(16), 5616-5622 (1998).
26. Gilon C, Halle D, Chorev M, Selinger Z, Byk G. Backbone cyclization: a new method for conferring conformational constraint on peptides. Biopolymers 31(6), 745-750 (1991).
27. Grdadolnik SG, Mierke DF, Byk G, Zeltser I, Gilon C, Kessler H. Comparison of the conformation of active and nonactive backbone cyclic analogs of substance P as a tool to elucidate features of the bioactive conformation: NMR and molecular dynamics in DMSO and water. J. Med. Chem. 37(14), 2145-2152 (1994).
28. Hariton-Gazal E, Friedler D, Friedler A, Zakai N, Gilon C, Loyter A. Inhibition of nuclear import by backbone cyclic peptidomimetics derived from the HIV-1 MA NLS sequence. Biochim. Biophys. Acta 1594(2), 234-242 (2002).
29. Hess S, Linde Y, Ovadia O et al. Backbone cyclic peptidomimetic melanocortin-4 receptor agonist as a novel orally administrated drug lead for treating obesity. J. Med. Chem. 51(4), 1026-1034 (2008).
30. Linde Y, Ovadia O, Safrai E et al. Structure- activity relationship and metabolic stability studies of backbone cyclization and N-methylation of melanocortin peptides. Biopolymers 90(5), 671-682 (2008).
31. Chin JW, Grotzfeld RM, Fabian MA, Schepartz A. Methodology for optimizing functional miniature proteins based on avian pancreatic polypeptide using phage display. Bioorg. Med. Chem. Lett. 11(12), 1501-1505 (2001).
32. Chin JW, Schepartz A. Concerted evolution of structure and function in a miniature protein. J. Am. Chem. Soc. 123(12), 2929-2930 (2001). (Pubitemid 32910738)
33. Chin JW, Schepartz A. Design and evolution of a miniature Bcl-2 binding protein Angew. Chem. Int. Ed. Engl. 40(20), 3806-3809 (2001).
34. Gemperli AC, Rutledge SE, Maranda A, Schepartz A. Paralog-selective ligands for Bcl-2 proteins. J. Am. Chem. Soc. 127(6), 1596-1597 (2005).
35. Kritzer JA, Zutshi R, Cheah M et al. Miniature protein inhibitors of the p53- hDM2 interaction. Chembiochem 7(1), 29-31 (2006).
36. Zinzalla G, Thurston D. Targeting protein- protein interactions for therapeutic intervention: a challenge for the future. Future Med. Chem. 1(1), 65-93 (2009).
37. Schafmeister C, Po J, Verdine GL. An all-hydrocarbon cross-linking system for enhancing the helicity and metabolic stability of peptides. J. Am. Chem. Soc. 122(24), 5891-5892 (2000).
38. Walensky LD, Kung AL, Escher I et al. Activation of apoptosis in vivo by a hydrocarbon-stapled BH3 helix. Science 305(5689), 1466-1470 (2004).
39. Liu J, Wang D, Zheng Q, Lu M, Arora PS. Atomic structure of a short a-helix stabilized by a main chain hydrogen-bond surrogate. J. Am. Chem. Soc. 130(13), 4334-4337 (2008).
40. Frank R. SPOT-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support. Tetrahedron 48(42), 9217-9232 (1992).
41. Cretich M, Damin F, Pirri G, Chiari M. Protein and peptide arrays: recent trends and new directions. Biomol. Eng. 23(2-3), 77-88 (2006).
42. Hilpert K, Winkler DF, Hancock RE. Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat. Protoc. 2(6), 1333-1349 (2007).
43. Pazgier M, Liu M, Zou G et al. Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX. Proc. Natl Acad. Sci. USA 106(12), 4665-4670 (2009).
44. Friedler A, Veprintsev DB, Rutherford T, Von Glos KI, Fersht AR. Binding of Rad51 and other peptide sequences to a promiscuous, highly electrostatic binding site in p53. J. Biol. Chem. 280(9), 8051-8059 (2005).
45. Hecht I, Rong J, Sampaio Al et al. A novel peptide agonist of formyl-peptide receptor-like 1 (ALX) displays anti-inflammatory and cardioprotective effects. J. Pharmacol. Exp. Ther. 328(2), 426-434 (2009).
46. Hansson LO, Friedler A, Freund S, Rudiger S, Fersht AR. Two sequence motifs from HIF-1a bind to the DNA-binding site of p53. Proc. Natl Acad. Sci. USA 99(16), 10305-10309 (2002).
47. Rudiger S, Buchberger A, Bukau B. Interaction of Hsp70 chaperones with substrates. Nat. Struct. Biol. 4(5), 342-349 (1997).
48. Rudiger S, Germeroth L, Schneider-Mergener J, Bukau B. Substrate specificity of the DnaK chaperone determined by screening cellulose-bound peptide libraries. EMBO. J. 16(7), 1501-1507 (1997).
49. Vega CA, Kurt N, Chen Z, Rudiger S, Cavagnero S. Binding specificity of an a-helical protein sequence to a full-length Hsp70 chaperone and its minimal substrate-binding domain. Biochemistry 45(46), 13835-13846 (2006).
50. Patzelt H, Rudiger S, Brehmer D et al. Binding specificity of Escherichia coli trigger factor. Proc. Natl Acad. Sci. USA 98(25), 14244-14249 (2001).
51. Knoblauch NT, Rudiger S, Schonfeld HJ, Driessen AJ, Schneider-Mergener J, Bukau B. Substrate specificity of the SecB chaperone. J. Biol. Chem. 274(48), 34219-34225 (1999).
52. Katz C, Benyamini H, Rotem S et al. Molecular basis of the interaction between the antiapoptotic Bcl-2 family proteins and the proapoptotic protein ASPP2. Proc. Natl Acad. Sci. USA 105(34), 12277-12282 (2008).
53. Benyamini H, Leonov H, Rotem S, Katz C, Arkin IT, Friedler A. A model for the interaction between NF-k-B and ASPP2 suggests an I-k-B-like binding mechanism. Proteins 77(3), 602-611 (2009).
54. Rotem S, Katz C, Benyamini H et al. The structure and interactions of the proline-rich domain of ASPP2. J. Biol. Chem. 283(27), 18990-18999 (2008).
55. Ma K, Forbes JG, Gutierrez-Cruz G, Wang K. Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways: the clustering of novel overlap ligand motifs in the elastic PEVK segment. J. Biol. Chem. 281(37), 27539-27556 (2006).
56. Teufel DP, Freund SM, Bycroft M, Fersht AR. Four domains of p300 each bind tightly to a sequence spanning both transactivation subdomains of p53. Proc. Natl Acad. Sci. USA 104(17), 7009-7014 (2007).
57. Schon O, Friedler A, Bycroft M, Freund SM, Fersht AR. Molecular mechanism of the interaction between MDM2 and p53. J. Mol. Biol. 323(3), 491-501 (2002).
58. Schon O, Friedler A, Freund S, Fersht AR. Binding of p53-derived ligands to MDM2 induces a variety of long range conformational changes. J. Mol. Biol. 336(1), 197-202 (2004).
59. Dalkas GA, Papakyriakou A, Vlamis-Gardikas A, Spyroulias GA. Insights into the anthrax lethal factor-substrate interaction and selectivity using docking and molecular dynamics simulations. Protein Sci. 18(8), 1774-1785 (2009).
60. Joshi M, Ebalunode JO, Briggs JM. Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates. Proteins 75(2), 323-335 (2009).
61. Turjanski AG, Hummer G, Gutkind JS. How mitogen-activated protein kinases recognize and phosphorylate their targets: a QM/MM study. J. Am. Chem. Soc. 131(17), 6141-6148 (2009).
62. Latzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kB-nuclear localization signals by IkBa and IkBb. J. Mol. Biol. 367(1), 262-274 (2007).
63. Yan Z, Tripet B, Hodges RS. Biophysical characterization of HRC peptide analogs interaction with heptad repeat regions of the SARS-coronavirus spike fusion protein core. J. Struct. Biol. 155(2), 162-175 (2006).
64. Brown CJ, Dastidar SG, See Hy et al. Rational design and biophysical characterization of thioredoxin-based aptamers: insights into peptide grafting. J. Mol. Biol. 395(4), 871-883 (2009).
65. Garcia-Saez AJ, Ries J, Orzaez M, Perez-Paya E, Schwille P. Membrane promotes tBID interaction with Bcl(XL). Nat. Struct. Mol. Biol. 16(11), 1178-1185 (2009).
66. Herrera E, Gomara MJ, Mazzini S, Ragg E, Haro I. Synthetic peptides of hepatitis G virus (GBV-C/HGV) in the selection of putative peptide inhibitors of the HIV-1 fusion peptide. J. Phys. Chem. B 113(20), 7383-7391 (2009).
67. Demers JP, Mittermaier A. Binding mechanism of an SH3 domain studied by NMR and ITC. J. Am. Chem. Soc. 131(12), 4355-4367 (2009).
68. Eichler J. Peptides as protein binding site mimetics. Curr. Opin. Chem. Biol. 12(6), 707-713 (2008).
69. Otvos L Jr, Terrasi M, Cascio S et al. Development of a pharmacologically improved peptide agonist of the leptin receptor. Biochim. Biophys. Acta. 1783(10), 1745-1754 (2008).
70. Ortiz AA, Milardo LF, Decarr LB et al. A novel long-acting selective neuropeptide Y2 receptor polyethylene glycol-conjugated peptide agonist reduces food intake and body weight and improves glucose metabolism in rodents. J. Pharmacol. Exp. Ther. 323(2), 692-700 (2007).
71. Murray JK, Gellman SH. Targeting protein-protein interactions: lessons from p53/MDM2. Biopolymers 88(5), 657-686 (2007).
72. Phan J, Li Z, Kasprzak A et al. Structure-based design of high-affinity peptides inhibiting the interaction of p53 with MDM2 and MDMX. J. Biol. Chem. 285(3), 2174-2183 (2009).
73. Zawahir Z, Neamati N. Inhibition of HIV-1 integrase activity by synthetic peptides derived from the HIV-1 HXB2 pol region of the viral genome. Bioorg. Med. Chem. Lett. 16(19), 5199-5202 (2006).
74. Shultz MD, Ham YW, Lee SG, Davis DA, Brown C, Chmielewski J. Small-molecule dimerization inhibitors of wild-type and mutant HIV protease: a focused library approach. J. Am. Chem. Soc. 126(32), 9886-9887 (2004).
75. Kota S, Coito C, Mousseau G, Lavergne JP, Strosberg AD. Peptide inhibitors of hepatitis C virus core oligomerization and virus production. J. Gen. Virol. 90(Pt 6), 1319-1328 (2009).
76. Moellering RE, Cornejo M, Davis TN et al. Direct inhibition of the NOTCH transcription factor complex. Nature 462(7270), 182-188 (2009).
77. Sudarman E, Bollati-Fogolin M, Hafner M et al. Synthetic mimetics of the gp130 binding site for viral interleukin-6 as inhibitors of the vIL-6-gp130 interaction. Chem. Biol. Drug Des. 71(5), 494-500 (2008).
78. Hayouka Z, Rosenbluh J, Levin A et al. Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium. Proc. Natl Acad. Sci. USA 104(20), 8316-8321 (2007).
79. Breinig S, Kervinen J, Stith L et al. Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase. Nat. Struct. Biol. 10(9), 757-763 (2003).
80. Jaffe EK. Morpheeins - a new structural paradigm for allosteric regulation. Trends Biochem. Sci. 30(9), 490-497 (2005).
81. Lawrence SH, Ramirez UD, Tang L et al. Shape shifting leads to small-molecule allosteric drug discovery. Chem. Biol. 15(6), 586-596 (2008).
82. Yu P, Pettigrew DW. Linkage between fructose 1,6-bisphosphate binding and the dimer-tetramer equilibrium of Escherichia coli glycerol kinase: critical behavior arising from change of ligand stoichiometry. Biochemistry 42(14), 4243-4252 (2003).
83. Hayouka Z, Rosenbluh J, Levin A, Maes M, Loyter A, Friedler A. Peptides derived from HIV-1 REV inhibit HIV-1 integrase in a shiftide mechanism. Biopolymers 90(4), 481-487 (2008).
84. Maes M, Levin A, Hayouka Z, Shalev DE, Loyter A, Friedler A. Peptide inhibitors of HIV-1 integrase: from mechanistic studies to improved lead compounds. Bioorg. Med. Chem. 17(22), 7635-7642 (2009).
85. Armon-Omer A, Levin A, Hayouka Z et al. Correlation between shiftide activity and HIV-1 integrase inhibition by a peptide selected from a combinatorial library. J. Mol. Biol. 376(4), 971-982 (2008).
86. Ronen D, Rosenberg MM, Shalev De et al. The positively charged region of the myosin IIC non-helical tailpiece promotes filament assembly. J. Biol. Chem. (2009).
87. Kolter T, Wendeler M. Chemical chaperones - a new concept in drug research. Chembiochem 4(4), 260-264 (2003).
88. Friedler A, Hansson LO, Veprintsev DB et al. A peptide that binds and stabilizes p53 core domain: chaperone strategy for rescue of oncogenic mutants. Proc. Natl Acad. Sci. USA 99(2), 937-942 (2002).
89. Friedler A, Dedecker BS, Freund SM, Blair C, Rudiger S, Fersht AR. Structural distortion of p53 by the mutation R249S and its rescue by a designed peptide: implications for 'mutant conformation'. J. Mol. Biol. 336(1), 187-196 (2004).
90. Kliger Y, Levy O, Oren A et al. Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept. Proc. Natl Acad. Sci. USA 106(33), 13797-13801 (2009).
91. Vagner J, Qu H, Hruby VJ. Peptidomimetics, a synthetic tool of drug discovery. Curr. Opin. Chem. Biol. 12(3), 292-296 (2008).
92. Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat. Rev. Drug Discov. 3(4), 301-317 (2004).
93. Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172), 1001-1009 (2007).
94. Fry DC. Drug-like inhibitors of protein- protein interactions: a structural examination of effective protein mimicry. Curr. Protein Pept. Sci. 9(3), 240-247 (2008).
95. Kelekar A, Chang BS, Harlan JE, Fesik SW, Thompson CB. Bad is a BH3 domain-containing protein that forms an inactivating dimer with Bcl-XL. Mol. Cell Biol. 17(12), 7040-7046 (1997).
96. Lee EF, Czabotar PE, Smith BJ et al. Crystal structure of ABT-737 complexed with Bcl-XL: implications for selectivity of antagonists of the Bcl-2 family. Cell Death Differ. 14(9), 1711-1713 (2007).
97. Yin H, Frederick KK, Liu D, Wand AJ, Degrado WF. Arylamide derivatives as peptidomimetic inhibitors of calmodulin. Org. Lett. 8(2), 223-225 (2006).
98. Sun H, Nikolovska-Coleska Z, Lu J et al. Design, synthesis, and characterization of a potent, nonpeptide, cell-permeable, bivalent Smac mimetic that concurrently targets both the BIR2 and BIR3 domains in XIAP. J. Am. Chem. Soc. 129(49), 15279-15294 (2007).
99. Yin H, Lee GI, Sedey Ka et al. Terphenyl-based bak BH3 a-helical proteomimetics as low-molecular-weight antagonists of Bcl-XL. J. Am. Chem. Soc. 127(29), 10191-10196 (2005).