High-throughput screening by nuclear magnetic resonance (HTS by NMR) for the identification of PPIs antagonists

Current Topics in Medicinal Chemistry

Volumn 15, Issue 20, 2015, Pages 2032-2042

  Wu, Bainan ^a   Barile, Elisa ^a   De, Surya K ^a   Wei, Jun ^a   Purves, Angela ^a   Pellecchia, Maurizio ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

Drug discovery; FBDD; FBLD; Fragment based drug design; HTS by NMR; Positional scanning; PPIs; Protein protein interactions

Indexed keywords

4 [4 (4' CHLORO 2 BIPHENYLYLMETHYL) 1 PIPERAZINYL] N [4 [3 DIMETHYLAMINO 1 (PHENYLTHIOMETHYL)PROPYLAMINO] 3 NITROBENZENESULFONYL]BENZAMIDE; PROTEIN BCL 2; PROTEIN BCL XL; PROTEIN INHIBITOR; PROTEIN MCL 1; PROTEIN PROTEIN INTERACTION ANTAGONIST; UNCLASSIFIED DRUG; VENETOCLAX; EPHRIN A5; EPHRIN RECEPTOR A4; LIGAND; MCL1 PROTEIN, HUMAN; MOLECULAR LIBRARY; PEPTIDE; PROTEIN BINDING; X LINKED INHIBITOR OF APOPTOSIS; XIAP PROTEIN, HUMAN;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CHEMICAL STRUCTURE; COMPUTER MODEL; DISSOCIATION CONSTANT; DRUG DESIGN; HIGH THROUGHPUT SCREENING; LIGAND BINDING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY; ANTAGONISTS AND INHIBITORS; CHEMISTRY; COMBINATORIAL CHEMISTRY; DRUG DEVELOPMENT; HUMAN; MOLECULAR LIBRARY; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN DOMAIN;

COMBINATORIAL CHEMISTRY TECHNIQUES; CRYSTALLOGRAPHY, X-RAY; DRUG DISCOVERY; EPHRIN-A5; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MYELOID CELL LEUKEMIA SEQUENCE 1 PROTEIN; PEPTIDES; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING; RECEPTOR, EPHA4; SMALL MOLECULE LIBRARIES; X-LINKED INHIBITOR OF APOPTOSIS PROTEIN;

EID: 84937115962     PISSN: 15680266     EISSN: 18734294     Source Type: Journal    
DOI: 10.2174/1568026615666150519102459     Document Type: Article

References (131)

1. Wells, J. A.; McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450 (7172), 1001-9
2. Arkin, M. R.; Wells, J. A. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat. Rev. Drug Discov., 2004, 3 (4), 301-17.
3. Bocker, A.; Bonneau, P. R.; Edwards, P. J. HTS promiscuity analyses for accelerating decision making. J Biomol. Screen, 2011, 16 (7), 765-74
4. Coan, K. E.; Maltby, D. A.; Burlingame, A. L.; Shoichet, B. K. Promiscuous aggregate-based inhibitors promote enzyme unfolding. J. Med. Chem., 2009, 52 (7), 2067-75
5. Baell, J. B.; Holloway, G. A. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J. Med. Chem., 2010, 53 (7), 2719-40
6. Rishton, G. M. Nonleadlikeness and leadlikeness in biochemical screening. Drug Discov. Today, 2003, 8 (2), 86-96
7. Hann, M. M.; Oprea, T. I. Pursuing the leadlikeness concept in pharmaceutical research. Curr. Opin. Chem. Biol., 2004, 8 (3), 255-63
8. Coan, K. E.; Shoichet, B. K. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol. Biosyst., 2007, 3 (3), 208-13
9. Feng, B. Y.; Shelat, A.; Doman, T. N.; Guy, R. K.; Shoichet, B. K. High-throughput assays for promiscuous inhibitors. Nat. Chem. Biol., 2005, 1 (3), 146-8
10. Feng, B. Y.; Shoichet, B. K. A detergent-based assay for the detection of promiscuous inhibitors. Nat. Protoc., 2006, 1 (2), 550-3
11. Feng, B. Y.; Shoichet, B. K. Synergy and antagonism of promiscuous inhibition in multiple-compound mixtures. J. Med. Chem., 2006, 49 (7), 2151-4
12. Feng, B. Y.; Simeonov, A.; Jadhav, A.; Babaoglu, K.; Inglese, J.; Shoichet, B. K.; Austin, C. P. A high-throughput screen for aggregation-based inhibition in a large compound library. J. Med. Chem., 2007, 50 (10), 2385-90
13. McGovern, S. L.; Helfand, B. T.; Feng, B.; Shoichet, B. K. A specific mechanism of nonspecific inhibition. J. Med. Chem., 2003, 46 (20), 4265-72
14. Seidler, J.; McGovern, S. L.; Doman, T. N.; Shoichet, B. K. Identification and prediction of promiscuous aggregating inhibitors among known drugs. J. Med. Chem., 2003, 46 (21), 4477-86
15. Shoichet, B. K. Interpreting steep doseresponse curves in early inhibitor discovery. J. Med. Chem., 2006, 49 (25), 7274-7.
16. Baell, J.; Walters, M. A. Chemistry: Chemical con artists foil drug discovery. Nature, 2014, 513 (7519), 481-3.
17. Pellecchia, M.; Meininger, D.; Dong, Q.; Chang, E.; Jack, R.; Sem, D. S. NMR-based structural characterization of large proteinligand interactions. J. Biomol. NMR, 2002, 22 (2), 165-73
18. Pellecchia, M. Solution nuclear magnetic resonance spectroscopy techniques for probing intermolecular interactions. Chem. Biol., 2005, 12 (9), 961-71
19. Stockman, B. J.; Dalvit, C. NMR screening techniques in drug discovery and drug design. Prog. Nucl. Magn. Reson. Spectrosc., 2002, 41, 187-231
20. Lepre, C. A.; Peng, J.; Fejzo, J.; Abdul-Manan, N.; Pocas, J.; Jacobs, M.; Xie, X.; Moore, J. M. Applications of SHAPES screening in drug discovery. Comb. Chem. High Throughput. Screen, 2002, 5 (8), 583-90
21. Wyss, D. F.; McCoy, M. A.; Senior, M. M. NMR-based approaches for lead discovery. Curr. Opin. Drug. Discov. Devel., 2002, 5 (4), 630-47
22. Jahnke, W.; Widmer, H. Protein NMR in biomedical research. Cell. Mol. Life Sci., 2004, 61 (5), 580-99
23. Huth, J. R.; Sun, C.; Sauer, D. R.; Hajduk, P. J. Utilization of NMR-derived fragment leads in drug design. Meth. Enzymol., 2005, 394, 549-71
24. Kessler, H.; Klages, J. Lead Search and Optimization: NMR in Drug Discovery. In Comprehensive Medicinal Chemistry II, Triggle, D. J.; Taylor, J. B., Eds. Elsevier, Oxford: 2006; Vol. 3, pp 901-920
25. Coles, M.; Heller, M.; Kessler, H. NMR-based screening technologies. Drug Discov. Today, 2003, 8 (17), 803-10
26. Luy, B.; Frank, A.; Kessler, H. Conformational analysis of drugs by NMR. In Molecular Drug Properties: Measurement and Prediction, Mannhold, R., Ed. Wiley-VCH, Weinheim: 2008; pp 207-254
27. Takeuchi, K.; Wagner, G. NMR studies of protein interactions. Curr. Opin. Struct. Biol., 2006, 16 (1), 109-17
28. Zartler, E. R.; Shapiro, M. J. Protein NMR-based screening in drug discovery. Curr. Pharm. Des. 2006, 12 (31), 3963-72
29. Fry, D. C.; Emerson, S. D. Applications of biomolecular NMR to drug discovery. Drug Des. Discov., 2000, 17 (1), 13-33
30. Salvatella, X.; Giralt, E. NMRbased methods and strategies for drug discovery. Chem. Soc. Rev., 2003, 32 (6), 365-72
31. Betz, M.; Saxena, K.; Schwalbe, H. Biomolecular NMR: a chaperone to drug discovery. Curr. Opin. Chem. Biol., 2006, 10 (3), 219-25
32. Klages, J.; Coles, M.; Kessler, H. NMR-based screening: a powerful tool in fragmentbased drug discovery. In NMR-Based Screening in Exploiting Chemical Diversity for Drug Discovery, Bartlett, P. A.; Etzeroth, M., Eds. RSC Publishing: 2006; Vol. 12, pp 263-290
33. Pellecchia, M.; Bertini, I.; Cowburn, D.; Dalvit, C.; Giralt, E.; Jahnke, W.; James, T. L.; Homans, S. W.; Kessler, H.; Luchinat, C.; Meyer, B.; Oschkinat, H.; Peng, J.; Schwalbe, H.; Siegal, G. Perspectives on NMR in drug discovery: a technique comes of age. Nat. Rev. Drug Discov., 2008, 7 (9), 738-45.
34. Barile, E.; Pellecchia, M. NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem. Rev., 2014, 114 (9), 4749-63.
35. Henchey, L. K.; Jochim, A. L.; Arora, P. S. Contemporary strategies for the stabilization of peptides in the alpha-helical conformation. Curr. Opin. Chem. Biol., 2008, 12 (6), 692-7.
36. Valkov, E.; Sharpe, T.; Marsh, M.; Greive, S.; Hyvonen, M. Targeting protein-protein interactions and fragment-based drug discovery. Top Curr. Chem., 2012, 317, 145-79
37. Zartler, E. R.; Shapiro, M. J. Fragonomics: fragment-based drug discovery. Curr. Opin. Chem. Biol., 2005, 9 (4), 366-70
38. Talamas, F. X.; Aoieong, G.; Brameld, K. A.; Chin, E.; de Vicente, J.; Dunn, J. P.; Ghate, M.; Giannetti, A. M.; Harris, S. F.; Labadie, S. S.; Leveque, V.; Li, J.; Lui, A. S.; McCaleb, K. L.; Najera, I.; Schoenfeld, R. C.; Wang, B.; Wong, A. De novo fragment design: a medicinal chemistry approach to fragment-based lead generation. J. Med. Chem., 2013, 56 (7), 3115-9
39. Fischer, M.; Hubbard, R. E. Fragment-based ligand discovery. Mol. Interv., 2009, 9 (1), 22-30
40. Rees, D. C.; Congreve, M.; Murray, C. W.; Carr, R. Fragmentbased lead discovery. Nat. Rev. Drug Discov., 2004, 3 (8), 660-72
41. Jahnke, W.; Erlanson, D. A. Fragment-based Approaches in Drug Discovery. Wiley-VCH: 2006.
42. Hajduk, P. J.; Sheppard, G.; Nettesheim, D. G.; Olejniczak, E. T.; Shuker, S. B.; Meadows, R. P.; Steinman, D. H.; Carrera, G. M.; Marcotte, P. A.; Severin, J.; Walter, K.; Smith, H.; Gubbins, E.; Simmer, R.; Holzman, T. F.; Morgan, D. W.; Davidsen, S. K.; Summers, J. B.; Fesik, S. W. Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J. Am. Chem. Soc., 1997, 119, 5818-5827
43. Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Discovering high-affinity ligands for proteins: SAR by NMR. Science 1996, 274 (5292), 1531-4.
44. Pellecchia, M. Antagonists of protein-protein interactions made easy? J. Med. Chem., 2013, 56 (1), 13-4.
45. Oltersdorf, T.; Elmore, S. W.; Shoemaker, A. R.; Armstrong, R. C.; Augeri, D. J.; Belli, B. A.; Bruncko, M.; Deckwerth, T. L.; Dinges, J.; Hajduk, P. J.; Joseph, M. K.; Kitada, S.; Korsmeyer, S. J.; Kunzer, A. R.; Letai, A.; Li, C.; Mitten, M. J.; Nettesheim, D. G.; Ng, S.; Nimmer, P. M.; O'Connor, J. M.; Oleksijew, A.; Petros, A. M.; Reed, J. C.; Shen, W.; Tahir, S. K.; Thompson, C. B.; Tomaselli, K. J.; Wang, B.; Wendt, M. D.; Zhang, H.; Fesik, S. W.; Rosenberg, S. H. An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 2005, 435 (7042), 677-81.
46. Vandenberg, C. J.; Cory, S. ABT-199, a new Bcl-2-specific BH3 mimetic, has in vivo efficacy against aggressive Myc-driven mouse lymphomas without provoking thrombocytopenia. Blood 2013, 121 (12), 2285-8
47. Souers, A. J.; Leverson, J. D.; Boghaert, E. R.; Ackler, S. L.; Catron, N. D.; Chen, J.; Dayton, B. D.; Ding, H.; Enschede, S. H.; Fairbrother, W. J.; Huang, D. C.; Hymowitz, S. G.; Jin, S.; Khaw, S. L.; Kovar, P. J.; Lam, L. T.; Lee, J.; Maecker, H. L.; Marsh, K. C.; Mason, K. D.; Mitten, M. J.; Nimmer, P. M.; Oleksijew, A.; Park, C. H.; Park, C. M.; Phillips, D. C.; Roberts, A. W.; Sampath, D.; Seymour, J. F.; Smith, M. L.; Sullivan, G. M.; Tahir, S. K.; Tse, C.; Wendt, M. D.; Xiao, Y.; Xue, J. C.; Zhang, H.; Humerickhouse, R. A.; Rosenberg, S. H.; Elmore, S. W. ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat. Med., 2013, 19 (2), 202-8.
48. Hamzeh-Mivehroud, M.; Alizadeh, A. A.; Morris, M. B.; Church, W. B.; Dastmalchi, S. Phage display as a technology delivering on the promise of peptide drug discovery. Drug Discov. Today, 2013, 18 (23-24), 1144-57
49. Tan, W. S.; Ho, K. L. Phage display creates innovative applications to combat hepatitis B virus. World journal of gastroenterology: WJG 2014, 20 (33), 11650-11670
50. Pande, J.; Szewczyk, M. M.; Grover, A. K. Phage display: concept, innovations, applications and future. Biotechnol. Adv., 2010, 28 (6), 849-58
51. Deutscher, S. L. Phage display in molecular imaging and diagnosis of cancer. Chem. Rev., 2010, 110 (5), 3196-211
52. Sidhu, S. S.; Koide, S. Phage display for engineering and analyzing protein interaction interfaces. Curr. Opin. Struct. Biol., 2007, 17 (4), 481-7
53. Brissette, R.; Prendergast, J. K.; Goldstein, N. I. Identification of cancer targets and therapeutics using phage display. Curr. Opin. Drug Discov. Devel., 2006, 9 (3), 363-9
54. Samoylova, T. I.; Morrison, N. E.; Globa, L. P.; Cox, N. R. Peptide phage display: opportunities for development of personalized anti-cancer strategies. Anticancer Agents Med. Chem., 2006, 6 (1), 9-17
55. Mullen, L. M.; Nair, S. P.; Ward, J. M.; Rycroft, A. N.; Henderson, B. Phage display in the study of infectious diseases. Trends Microbiol., 2006, 14 (3), 141-7
56. Paschke, M. Phage display systems and their applications. Appl. Microbiol. Biotechnol., 2006, 70 (1), 2-11
57. Kehoe, J. W.; Kay, B. K. Filamentous phage display in the new millennium. Chem. Rev., 2005, 105 (11), 4056-72.
58. Flygare, J. A.; Beresini, M.; Budha, N.; Chan, H.; Chan, I. T.; Cheeti, S.; Cohen, F.; Deshayes, K.; Doerner, K.; Eckhardt, S. G.; Elliott, L. O.; Feng, B.; Franklin, M. C.; Reisner, S. F.; Gazzard, L.; Halladay, J.; Hymowitz, S. G.; La, H.; LoRusso, P.; Maurer, B.; Murray, L.; Plise, E.; Quan, C.; Stephan, J. P.; Young, S. G.; Tom, J.; Tsui, V.; Um, J.; Varfolomeev, E.; Vucic, D.; Wagner, A. J.; Wallweber, H. J.; Wang, L.; Ware, J.; Wen, Z.; Wong, H.; Wong, J. M.; Wong, M.; Wong, S.; Yu, R.; Zobel, K.; Fairbrother, W. J. Discovery of a potent small-molecule antagonist of inhibitor of apoptosis (IAP) proteins and clinical candidate for the treatment of cancer (GDC-0152). J. Med. Chem., 2012, 55 (9), 4101-13.
59. Wu, B.; Zhang, Z.; Noberini, R.; Barile, E.; Giulianotti, M.; Pinilla, C.; Houghten, R. A.; Pasquale, E. B.; Pellecchia, M. HTS by NMR of combinatorial libraries: a fragment-based approach to ligand discovery. Chem. Biol., 2013, 20 (1), 19-33.
60. Dooley, C. T.; Houghten, R. A. Synthesis and screening of positional scanning combinatorial libraries. Methods Mol. Biol., 1998, 87, 13-24
61. Dooley, C. T.; Houghten, R. A. The use of positional scanning synthetic peptide combinatorial libraries for the rapid determination of opioid receptor ligands. Life Sci., 1993, 52 (18), 1509-17
62. Houghten, R. A.; Ostresh, J. M.; Pratt, S. M. Modified solid-phase methods for the rapid synthesis of opioid peptides. NIDA Res. Monogr., 1991, 112, 239-55
63. Pinilla, C.; Appel, J. R.; Blanc, P.; Houghten, R. A. Rapid identification of high affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries. BioTechniques, 1992, 13 (6), 901-5.
64. Klages, J.; Coles, M.; Kessler, H. NMR-based Screening. RSC Publishing: 2006; Vol. 12, p 263-290.
65. Gal, M.; Schanda, P.; Brutscher, B.; Frydman, L. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. J. Am. Chem. Soc. 2007, 129 (5), 1372-7
66. Schanda, P.; Kupce, E.; Brutscher, B. SOFAST-HMQC experiments for recording two-dimensional heteronuclear correlation spectra of proteins within a few seconds. J. Biomol. NMR ,2005, 33 (4), 199-211.
67. Pervushin, K.; Riek, R.; Wider, G.; Wuthrich, K. Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. U.S.A. 1997, 94 (23), 12366-71.
68. Religa, T. L.; Kay, L. E. Optimal methyl labeling for studies of supra-molecular systems. J. Biomol. NMR 2010, 47 (3), 163-9
69. Tugarinov, V.; Kanelis, V.; Kay, L. E. Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat. Protoc., 2006, 1 (2), 749-54
70. Goto, N. K.; Gardner, K. H.; Mueller, G. A.; Willis, R. C.; Kay, L. E. A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15N-, 13C-, 2H-labeled proteins. J. Biomol. NMR, 1999, 13 (4), 369-74
71. Rosen, M. K.; Gardner, K. H.; Willis, R. C.; Parris, W. E.; Pawson, T.; Kay, L. E. Selective methyl group protonation of perdeuterated proteins. J. Mol. Biol., 1996, 263 (5), 627-36.
72. Pellecchia, M.; Sem, D. S.; Wuthrich, K. NMR in drug discovery. Nat. Rev. Drug Discov., 2002, 1 (3), 211-9.
73. Giannetti, A. M. From experimental design to validated hits a comprehensive walk-through of fragment lead identification using surface plasmon resonance. Meth. Enzymol., 2011, 493, 169-218
74. Frostell, A.; Vinterback, L.; Sjobom, H. Protein-Ligand Interactions Using SPR Systems. Methods Mol. Biol., 2013, 1008, 139-65
75. Elinder, M.; Geitmann, M.; Gossas, T.; Kallblad, P.; Winquist, J.; Nordstrom, H.; Hamalainen, M.; Danielson, U. H. Experimental validation of a fragment library for lead discovery using SPR biosensor technology. J Biomol Screen, 2011, 16 (1), 15-25
76. Danielson, U. H. Fragment library screening and lead characterization using SPR biosensors. Curr. Top. Med. Chem., 2009, 9 (18), 1725-35
77. Torres, F. E.; Recht, M. I.; Coyle, J. E.; Bruce, R. H.; Williams, G. Higher throughput calorimetry: opportunities, approaches and challenges. Curr. Opin. Struct. Biol., 2010, 20 (5), 598-605.
78. Chen, Y.; Shoichet, B. K. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat. Chem. Biol., 2009, 5 (5), 358-64
79. Clark, M.; Meshkat, S.; Talbot, G. T.; Carnevali, P.; Wiseman, J. S. Fragment-based computation of binding free energies by systematic sampling. J. Chem. Inf. Model, 2009, 49 (8), 1901-13.
80. Recht, M. I.; Sridhar, V.; Badger, J.; Hernandez, L.; Chie-Leon, B.; Nienaber, V.; Torres, F. E. Fragment-based screening for inhibitors of PDE4A using enthalpy arrays and X-ray crystallography. J. Biomol. Screen, 2012, 17 (4), 469-80
81. Hennig, M.; Ruf, A.; Huber, W. Combining biophysical screening and X-ray crystallography for fragment-based drug discovery. Top. Curr. Chem., 2012, 317, 115-43
82. Wyss, D. F.; Wang, Y. S.; Eaton, H. L.; Strickland, C.; Voigt, J. H.; Zhu, Z.; Stamford, A. W. Combining NMR and X-ray crystallography in fragment-based drug discovery: discovery of highly potent and selective BACE-1 inhibitors. Top. Curr. Chem., 2012, 317, 83-114
83. Wang, Y. S.; Strickland, C.; Voigt, J. H.; Kennedy, M. E.; Beyer, B. M.; Senior, M. M.; Smith, E. M.; Nechuta, T. L.; Madison, V. S.; Czarniecki, M.; McKittrick, B. A.; Stamford, A. W.; Parker, E. M.; Hunter, J. C.; Greenlee, W. J.; Wyss, D. F. Application of fragment-based NMR screening, X-ray crystallography, structure-based design, and focused chemical library design to identify novel microM leads for the development of nM BACE-1 (beta-site APP cleaving enzyme 1) inhibitors. J. Med. Chem., 2010, 53 (3), 942-50
84. Jhoti, H.; Cleasby, A.; Verdonk, M.; Williams, G. Fragment-based screening using X-ray crystallography and NMR spectroscopy. Curr. Opin. Chem. Biol., 2007, 11 (5), 485-93
85. Gill, A.; Cleasby, A.; Jhoti, H. The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography. Chembiochem., 2005, 6 (3), 506-12
86. Hartshorn, M. J.; Murray, C. W.; Cleasby, A.; Frederickson, M.; Tickle, I. J.; Jhoti, H. Fragment-based lead discovery using X-ray crystallography. J. Med. Chem., 2005, 48 (2), 403-13
87. Lesuisse, D.; Lange, G.; Deprez, P.; Benard, D.; Schoot, B.; Delettre, G.; Marquette, J. P.; Broto, P.; Jean-Baptiste, V.; Bichet, P.; Sarubbi, E.; Mandine, E. SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2. J. Med. Chem., 2002, 45 (12), 2379-87.
88. Petros, A. M.; Dinges, J.; Augeri, D. J.; Baumeister, S. A.; Betebenner, D. A.; Bures, M. G.; Elmore, S. W.; Hajduk, P. J.; Joseph, M. K.; Landis, S. K.; Nettesheim, D. G.; Rosenberg, S. H.; Shen, W.; Thomas, S.; Wang, X.; Zanze, I.; Zhang, H.; Fesik, S. W. Discovery of a potent inhibitor of the antiapoptotic protein BclxL from NMR and parallel synthesis. J. Med. Chem., 2006, 49 (2), 656-63.
89. Mok, W. W.; Li, Y. Therapeutic peptides: new arsenal against drug resistant pathogens. Curr. Pharm. Des., 2014, 20 (5), 771-92
90. Farkhani, S. M.; Valizadeh, A.; Karami, H.; Mohammadi, S.; Sohrabi, N.; Badrzadeh, F. Cell penetrating peptides: efficient vectors for delivery of nanoparticles, nanocarriers, therapeutic and diagnostic molecules. Peptides, 2014, 57, 78-94
91. Vasconcelos, L.; Parn, K.; Langel, U. Therapeutic potential of cell-penetrating peptides. Ther. Deliv., 2013, 4 (5), 573-91
92. Joo, S. H. Cyclic peptides as therapeutic agents and biochemical tools. Biomol. Ther., (Seoul) 2012, 20 (1), 19-26
93. Boohaker, R. J.; Lee, M. W.; Vishnubhotla, P.; Perez, J. M.; Khaled, A. R. The use of therapeutic peptides to target and to kill cancer cells. Curr. Med. Chem., 2012, 19 (22), 3794-804
94. Lindberg, S.; Copolovici, D. M.; Langel, U. Therapeutic delivery opportunities, obstacles and applications for cell-penetrating peptides. Ther. Deliv., 2011, 2 (1), 71-82
95. Johnson, R. M.; Harrison, S. D.; Maclean, D. Therapeutic applications of cell-penetrating peptides. Methods Mol. Biol., 2011, 683, 535-51
96. Mason, J. M. Design and development of peptides and peptide mimetics as antagonists for therapeutic intervention. Future Med. Chem., 2010, 2 (12), 1813-22
97. Juliano, R. L.; Alam, R.; Dixit, V.; Kang, H. M. Cell-targeting and cell-penetrating peptides for delivery of therapeutic and imaging agents. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 2009, 1 (3), 324-35
98. Bidwell, G. L.; Raucher, D. Therapeutic peptides for cancer therapy. Part I - peptide inhibitors of signal transduction cascades. Expert. Opin. Drug Deliv., 2009, 6 (10), 1033-47.
99. Lee, S.; Braun, C. R.; Bird, G. H.; Walensky, L. D. Photoreactive stapled peptides to identify and characterize BCL-2 family interaction sites by mass spectrometry. Meth. Enzymol., 2014, 544, 25-48
100. Walensky, L. D.; Bird, G. H. Hydrocarbonstapled peptides: principles, practice, and progress. J. Med. Chem., 2014, 57 (15), 6275-88
101. Bird, G. H.; Gavathiotis, E.; LaBelle, J. L.; Katz, S. G.; Walensky, L. D. Distinct BimBH3 (BimSAHB) stapled peptides for structural and cellular studies. ACS Chem. Biol., 2014, 9 (3), 831-7
102. Nomura, W.; Aikawa, H.; Ohashi, N.; Urano, E.; Metifiot, M.; Fujino, M.; Maddali, K.; Ozaki, T.; Nozue, A.; Narumi, T.; Hashimoto, C.; Tanaka, T.; Pommier, Y.; Yamamoto, N.; Komano, J. A.; Murakami, T.; Tamamura, H. Cellpermeable stapled peptides based on HIV-1 integrase inhibitors derived from HIV-1 gene products. ACS Chem. Biol., 2013, 8 (10), 2235-44
103. Demizu, Y.; Nagoya, S.; Shirakawa, M.; Kawamura, M.; Yamagata, N.; Sato, Y.; Doi, M.; Kurihara, M. Development of stapled short helical peptides capable of inhibiting vitamin D receptor (VDR)-coactivator interactions. Bioorg. Med. Chem. Lett., 2013, 23 (15), 4292-6
104. Verdine, G. L.; Hilinski, G. J. Stapled peptides for intracellular drug targets. Meth. Enzymol., 2012, 503, 3-33.
105. Winter, G.; Griffiths, A. D.; Hawkins, R. E.; Hoogenboom, H. R. Making antibodies by phage display technology. Annu. Rev. Immunol., 1994, 12, 433-55
106. Smith, G. P.; Petrenko, V. A. Phage Display. Chem. Rev., 1997, 97 (2), 391-410.
107. Heinis, C.; Rutherford, T.; Freund, S.; Winter, G. Phageencoded combinatorial chemical libraries based on bicyclic peptides. Nat. Chem. Biol., 2009, 5 (7), 502-7
108. Landon, L. A.; Deutscher, S. L. Combinatorial discovery of tumor targeting peptides using phage display. J. Cell. Biochem., 2003, 90 (3), 509-17.
109. Nefzi, A.; Ostresh, J. M.; Yu, Y.; Houghten, R. A. Combinatorial chemistry: libraries from libraries, the art of the diversity-oriented transformation of resin-bound peptides and chiral polyamides to low molecular weight acyclic and heterocyclic compounds. J. Org. Chem., 2004, 69 (11), 3603-9
110. Hoesl, C. E.; Nefzi, A.; Ostresh, J. M.; Yu, Y.; Houghten, R. A. Mixture-based combinatorial libraries: from peptides and peptidomimetics to small molecule acyclic and heterocyclic compounds. Meth. Enzymol., 2003, 369, 496-517
111. Dooley, C. T.; Houghten, R. A. New opioid peptides, peptidomimetics, and heterocyclic compounds from combinatorial libraries. Biopolymers, 1999, 51 (6), 379-90
112. Nefzi, A.; Dooley, C.; Ostresh, J. M.; Houghten, R. A. Combinatorial chemistry: from peptides and peptidomimetics to small organic and heterocyclic compounds. Bioorg. Med. Chem. Lett., 1998, 8 (17), 2273-8
113. Blondelle, S. E.; Takahashi, E.; Weber, P. A.; Houghten, R. A. Identification of antimicrobial peptides by using combinatorial libraries made up of unnatural amino acids. Antimicrob. Agents Chemother., 1994, 38 (10), 2280-6
114. Houghten, R. A.; Appel, J. R.; Blondelle, S. E.; Cuervo, J. H.; Dooley, C. T.; Pinilla, C. The use of synthetic peptide combinatorial libraries for the identification of bioactive peptides. BioTechniques, 1992, 13 (3), 412-21
115. Wang, J.; Anania, V. G.; Knott, J.; Rush, J.; Lill, J. R.; Bourne, P. E.; Bandeira, N. Combinatorial approach for large-scale identification of linked peptides from tandem mass spectrometry spectra. Mol. Cell Proteomics, 2014, 13 (4), 1128-36
116. Gray, B. P.; Brown, K. C. Combinatorial peptide libraries: mining for cell-binding peptides. Chem. Rev., 2014, 114 (2), 1020-81
117. Bohrer, B. C.; Li, Y. F.; Reilly, J. P.; Clemmer, D. E.; DiMarchi, R. D.; Radivojac, P.; Tang, H.; Arnold, R. J. Combinatorial libraries of synthetic peptides as a model for shotgun proteomics. Anal. Chem. 2010, 82 (15), 6559-68
118. Aina, O. H.; Liu, R.; Sutcliffe, J. L.; Marik, J.; Pan, C. X.; Lam, K. S. From combinatorial chemistry to cancertargeting peptides. Mol. Pharm., 2007, 4 (5), 631-51
119. Bersanetti, P. A.; Andrade, M. C.; Casarini, D. E.; Juliano, M. A.; Nchinda, A. T.; Sturrock, E. D.; Juliano, L.; Carmona, A. K. Positional-scanning combinatorial libraries of fluorescence resonance energy transfer peptides for defining substrate specificity of the angiotensin I-converting enzyme and development of selective C-domain substrates. Biochemistry, 2004, 43 (50), 15729-36
120. Real, E.; Rain, J. C.; Battaglia, V.; Jallet, C.; Perrin, P.; Tordo, N.; Chrisment, P.; D'Alayer, J.; Legrain, P.; Jacob, Y. Antiviral drug discovery strategy using combinatorial libraries of structurally constrained peptides. J. Virol., 2004, 78 (14), 7410-7
121. Boon, C. L.; Frost, D.; Chakrabartty, A. Identification of stable helical bundles from a combinatorial library of amphipathic peptides. Biopolymers, 2004, 76 (3), 244-57
122. Cowell, S. M.; Gu, X.; Vagner, J.; Hruby, V. J. Intelligent design in combinatorial chemistry: use of designed peptide libraries to explore secondary and tertiary structures in peptides and proteins. Meth. Enzymol., 2003, 369, 288-97
123. Nefzi, A.; Ostresh, J. M.; Houghten, R. A. Combinatorial chemistry: mixture-based combinatorial libraries of acyclic and heterocyclic compounds from amino acids and short peptides. EXS, 2003, (93), 109-23
124. Horton, D. A.; Bourne, G. T.; Smythe, M. L. Exploring privileged structures: the combinatorial synthesis of cyclic peptides. Mol. Divers., 2002, 5 (4), 289-304.
125. Dooley, C. T.; Kaplan, R. A.; Chung, N. N.; Schiller, P. W.; Bidlack, J. M.; Houghten, R. A. Six highly active mu-selective opioid peptides identified from two synthetic combinatorial libraries. Pept. Res., 1995, 8 (3), 124-37.
126. Lamberto, I.; Qin, H.; Noberini, R.; Premkumar, L.; Bourgin, C.; Riedl, S. J.; Song, J.; Pasquale, E. B. Distinctive binding of three antagonistic peptides to the ephrin-binding pocket of the EphA4 receptor. Biochem. J., 2012, 445 (1), 47-56
127. Lamberto, I.; Lechtenberg, B. C.; Olson, E. J.; Mace, P. D.; Dawson, P. E.; Riedl, S. J.; Pasquale, E. B. Development and Structural Analysis of a Nanomolar Cyclic Peptide Antagonist for the EphA4 Receptor. ACS Chem. Biol., 2014.
128. Noberini, R.; Koolpe, M.; Peddibhotla, S.; Dahl, R.; Su, Y.; Cosford, N. D.; Roth, G. P.; Pasquale, E. B. Small molecules can selectively inhibit ephrin binding to the EphA4 and EphA2 receptors. J. Biol. Chem., 2008, 283 (43), 29461-72.
129. Joseph, T. L.; Lane, D. P.; Verma, C. S. Stapled BH3 peptides against MCL-1: mechanism and design using atomistic simulations. PloS one, 2012, 7 (8), e43985.
130. Houghten, R. A.; Pinilla, C.; Appel, J. R.; Blondelle, S. E.; Dooley, C. T.; Eichler, J.; Nefzi, A.; Ostresh, J. M. Mixture-based synthetic combinatorial libraries. J. Med. Chem., 1999, 42 (19), 3743-78
131. Pinilla, C.; Appel, J.; Blondelle, S.; Dooley, C.; Dorner, B.; Eichler, J.; Ostresh, J.; Houghten, R. A. A review of the utility of soluble peptide combinatorial libraries. Biopolymers, 1995, 37 (3), 221-40.