Fine-tuning multiprotein complexes using small molecules

ACS Chemical Biology

Volumn 7, Issue 8, 2012, Pages 1311-1320

  Thompson, Andrea D ^a   Dugan, Amanda ^a   Gestwicki, Jason E ^a   Mapp, Anna K ^a,b  

^a Life Sciences Institute   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; INDUCIBLE NITRIC OXIDE SYNTHASE; MULTIPROTEIN COMPLEX; PROTEIN KINASE B; TRANSLOCON; VASCULAR CELL ADHESION MOLECULE 1;

ACETYLATION; ALLOSTERISM; ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; ENDOPLASMIC RETICULUM; GLYCOSYLATION; MOLECULAR LIBRARY; NEDDYLATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; UBIQUITINATION;

ALLOSTERIC SITE; ANIMALS; DRUG DESIGN; HUMANS; LIGANDS; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 84865203739     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb300255p     Document Type: Article

References (116)

1. Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network Nature 437, 1173-1178
2. Hopkins, A. L. and Groom, C. R. (2002) The druggable genome Nat. Rev. Drug Discovery 1, 727-730
3. Cravatt, B. F., Simon, G. M., and Yates, J. R., 3rd (2007) The biological impact of mass-spectrometry-based proteomics Nature 450, 991-1000
4. Powers, E. T., Morimoto, R. I., Dillin, A., Kelly, J. W., and Balch, W. E. (2009) Biological and chemical approaches to diseases of proteostasis deficiency Annu. Rev. Biochem. 78, 959-991
5. Surade, S. and Blundell, T. L. (2012) Structural biology and drug discovery of difficult targets: the limits of ligandability Chem. Biol. 19, 42-50
6. Overington, J. P., Al-Lazikani, B., and Hopkins, A. L. (2006) How many drug targets are there? Nat. Rev. Drug Discovery 5, 993-996
7. Drews, J. (2000) Drug discovery: a historical perspective Science 287, 1960-1964
8. Stumpf, M. P., Thorne, T., de Silva, E., Stewart, R., An, H. J., Lappe, M., and Wiuf, C. (2008) Estimating the size of the human interactome Proc. Natl. Acad. Sci. U.S.A. 105, 6959-6964
9. Wells, J. A. and McClendon, C. L. (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces Nature 450, 1001-1009
10. Bourgeas, R., Basse, M. J., Morelli, X., and Roche, P. (2010) Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database PLoS One 5, e9598
11. Higueruelo, A. P., Schreyer, A., Bickerton, G. R., Pitt, W. R., Groom, C. R., and Blundell, T. L. (2009) Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database Chem. Biol. Drug Des. 74, 457-467
12. Romero, G., von Zastrow, M., and Friedman, P. A. (2011) Role of PDZ proteins in regulating trafficking, signaling, and function of GPCRs: means, motif, and opportunity Adv. Pharmacol. 62, 279-314
13. Hohfeld, J., Cyr, D. M., and Patterson, C. (2001) From the cradle to the grave: molecular chaperones that may choose between folding and degradation EMBO Rep. 2, 885-890
14. Young, A., Lyons, J., Miller, A. L., Phan, V. T., Alarcon, I. R., and McCormick, F. (2009) Ras signaling and therapies Adv. Cancer Res. 102, 1-17
15. Lessard, J., Wu, J. I., Ranish, J. A., Wan, M., Winslow, M. M., Staahl, B. T., Wu, H., Aebersold, R., Graef, I. A., and Crabtree, G. R. (2007) An essential switch in subunit composition of a chromatin remodeling complex during neural development Neuron 55, 201-215
16. Yoo, A. S. and Crabtree, G. R. (2009) ATP-dependent chromatin remodeling in neural development Curr. Opin. Neurobiol. 19, 120-126
17. Perot, S., Sperandio, O., Miteva, M. A., Camproux, A. C., and Villoutreix, B. O. (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery Drug Discovery Today 15, 656-667
18. Fuller, J. C., Burgoyne, N. J., and Jackson, R. M. (2009) Predicting druggable binding sites at the protein-protein interface Drug Discovery Today 14, 155-161
19. DeLano, W. L. (2002) Unraveling hot spots in binding interfaces: progress and challenges Curr. Opin. Struct. Biol. 12, 14-20
20. Lo Conte, L., Chothia, C., and Janin, J. (1999) The atomic structure of protein-protein recognition sites J. Mol. Biol. 285, 2177-2198
21. Nooren, I. M. and Thornton, J. M. (2003) Diversity of protein-protein interactions EMBO J. 22, 3486-3492
22. Nooren, I. M. and Thornton, J. M. (2003) Structural characterisation and functional significance of transient protein-protein interactions J. Mol. Biol. 325, 991-1018
23. Wang, L., Liu, Y. T., Hao, R., Chen, L., Chang, Z., Wang, H. R., Wang, Z. X., and Wu, J. W. (2011)) Molecular mechanism of the negative regulation of Smad1/5 protein by carboxyl terminus of Hsc70-interacting protein (CHIP) J. Biol. Chem. 286, 15883-15894
24. Jiang, J., Maes, E. G., Taylor, A. B., Wang, L., Hinck, A. P., Lafer, E. M., and Sousa, R. (2007) Structural basis of J cochaperone binding and regulation of Hsp70 Mol. Cell 28, 422-433
25. Schuermann, J. P., Jiang, J., Cuellar, J., Llorca, O., Wang, L., Gimenez, L. E., Jin, S., Taylor, A. B., Demeler, B., Morano, K. A., Hart, P. J., Valpuesta, J. M., Lafer, E. M., and Sousa, R. (2008) Structure of the Hsp110:Hsc70 nucleotide exchange machine Mol. Cell 31, 232-243
26. Ahmad, A., Bhattacharya, A., McDonald, R. A., Cordes, M., Ellington, B., Bertelsen, E. B., and Zuiderweg, E. R. (2011) Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface Proc. Natl. Acad. Sci. U.S.A. 108, 18966-18971
27. Zhu, X., Zhao, X., Burkholder, W. F., Gragerov, A., Ogata, C. M., Gottesman, M. E., and Hendrickson, W. A. (1996) Structural analysis of substrate binding by the molecular chaperone DnaK Science 272, 1606-1614
28. Scheufler, C., Brinker, A., Bourenkov, G., Pegoraro, S., Moroder, L., Bartunik, H., Hartl, F. U., and Moarefi, I. (2000) Structure of TPR domain-peptide complexes: critical elements in the assembly of the Hsp70-Hsp90 multichaperone machine Cell 101, 199-210
29. Feng, H., Jenkins, L. M., Durell, S. R., Hayashi, R., Mazur, S. J., Cherry, S., Tropea, J. E., Miller, M., Wlodawer, A., Appella, E., and Bai, Y. (2009) Structural basis for p300 Taz2-p53 TAD1 binding and modulation by phosphorylation Structure 17, 202-210
30. Lee, W., Harvey, T. S., Yin, Y., Yau, P., Litchfield, D., and Arrowsmith, C. H. (1994) Solution structure of the tetrameric minimum transforming domain of p53 Nat. Struct. Biol. 1, 877-890
31. Popowicz, G. M., Czarna, A., and Holak, T. A. (2008) Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain Cell Cycle 7, 2441-2443
32. Lee, C. W., Martinez-Yamout, M. A., Dyson, H. J., and Wright, P. E. (2010) Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein Biochemistry 49, 9964-9971
33. Patel, S. D., Ciatto, C., Chen, C. P., Bahna, F., Rajebhosale, M., Arkus, N., Schieren, I., Jessell, T. M., Honig, B., Price, S. R., and Shapiro, L. (2006) Type II cadherin ectodomain structures: implications for classical cadherin specificity Cell 124, 1255-1268
34. Stauber, D. J., Debler, E. W., Horton, P. A., Smith, K. A., and Wilson, I. A. (2006) Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor Proc. Natl. Acad. Sci. U.S.A. 103, 2788-2793
35. Sun, H., Stuckey, J. A., Nikolovska-Coleska, Z., Qin, D., Meagher, J. L., Qiu, S., Lu, J., Yang, C. Y., Saito, N. G., and Wang, S. (2008)) Structure-based design, synthesis, evaluation, and crystallographic studies of conformationally constrained Smac mimetics as inhibitors of the X-linked inhibitor of apoptosis protein (XIAP) J. Med. Chem. 51, 7169-7180
36. Wu, G., Chai, J., Suber, T. L., Wu, J. W., Du, C., Wang, X., and Shi, Y. (2000) Structural basis of IAP recognition by Smac/DIABLO Nature 408, 1008-1012
37. Vaynberg, J., Fukuda, T., Chen, K., Vinogradova, O., Velyvis, A., Tu, Y., Ng, L., Wu, C., and Qin, J. (2005) Structure of an ultraweak protein-protein complex and its crucial role in regulation of cell morphology and motility Mol. Cell 17, 513-523
38. Arkin, M. R. and Wells, J. A. (2004) Small-molecule inhibitors of protein-protein interactions: progressing towards the dream Nat. Rev. Drug Discovery 3, 301-317
39. Lipinski, C. and Hopkins, A. (2004) Navigating chemical space for biology and medicine Nature 432, 855-861
40. Lipinski, C. A. (2000) Drug-like properties and the causes of poor solubility and poor permeability J. Pharmacol. Toxicol. Methods 44, 235-249
41. Lindsley, J. E. and Rutter, J. (2006) Whence cometh the allosterome? Proc. Natl. Acad. Sci. U.S.A. 103, 10533-10535
42. Jiang, F., Frey, B. R., Evans, M. L., Friel, J. C., and Hopper, J. E. (2009) Gene activation by dissociation of an inhibitor from a transcriptional activation domain Mol. Cell. Biol. 29, 5604-5610
43. Weinkam, P., Pons, J., and Sali, A. (2012) Structure-based model of allostery predicts coupling between distant sites Proc. Natl. Acad. Sci. U.S.A. 109, 4875-5880
44. Kenakin, T. P. (2010) Ligand detection in the allosteric world J. Biomol. Screening 15, 119-130
45. Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M., and Snyder, M. (2010) Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses Cell 143, 639-650
46. Lawrence, S. H., Ramirez, U. D., Tang, L., Fazliyez, F., Kundrat, L., Markham, G. D., and Jaffe, E. K. (2008) Shape shifting leads to small-molecule allosteric drug discovery Chem. Biol. 15, 586-596
47. Lawrence, S. H., Ramirez, U. D., Selwood, T., Stith, L., and Jaffe, E. K. (2009) Allosteric inhibition of human porphobilinogen synthase J. Biol. Chem. 284, 35807-35817
48. Roman, D. L., Blazer, L. L., Monroy, C. A., and Neubig, R. R. (2010) Allosteric inhibition of the regulator of G protein signaling-Galpha protein-protein interaction by CCG-4986 Mol. Pharmacol. 78, 360-365
49. Mallya, M., Phillips, R. L., Saldanha, S. A., Gooptu, B., Brown, S. C., Termine, D. J., Shirvani, A. M., Wu, Y., Sifers, R. N., Abagyan, R., and Lomas, D. A. (2007) Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates J. Med. Chem. 50, 5357-5363
50. Blazer, L. L., Roman, D. L., Chung, A., Larsen, M. J., Greedy, B. M., Husbands, S. M., and Neubig, R. R. (2010) Reversible, allosteric small-molecule inhibitors of regulator of G protein signaling proteins Mol. Pharmacol. 78, 524-533
51. Chang, L., Miyata, Y., Ung, P. M., Bertelsen, E. B., McQuade, T. J., Carlson, H. A., Zuiderweg, E. R., and Gestwicki, J. E. (2011) Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism Chem. Biol. 18, 210-221
52. McMillan, K., Adler, M., Auld, D. S., Baldwin, J. J., Blasko, E., Browne, L. J., Chelsky, D., Davey, D., Dolle, R. E., Eagen, K. A., Erickson, S., Feldman, R. I., Glaser, C. B., Mallari, C., Morrissey, M. M., Ohlmeyer, M. H., Pan, G., Parkinson, J. F., Phillips, G. B., Polokoff, M. A., Sigal, N. H., Vergona, R., Whitlow, M., Young, T. A., and Devlin, J. J. (2000) Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry Proc. Natl. Acad. Sci. U.S.A. 97, 1506-1511
53. Conn, P. J., Christopoulos, A., and Lindsley, C. W. (2009) Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders Nat. Rev. Drug Discovery 8, 41-54
54. Osborne, A. R., Rapoport, T. A., and van den Berg, B. (2005) Protein translocation by the Sec61/SecY channel Annu. Rev. Cell. Dev. Biol. 21, 529-550
55. Kim, S. J., Mitra, D., Salerno, J. R., and Hegde, R. S. (2002) Signal sequences control gating of the protein translocation channel in a substrate-specific manner Dev. Cell. 2, 207-217
56. Rutkowski, D. T., Lingappa, V. R., and Hegde, R. S. (2001) Substrate-specific regulation of the ribosome- translocon junction by N-terminal signal sequences Proc. Natl. Acad. Sci. U.S.A. 98, 7823-7828
57. Garrison, J. L., Kunkel, E. J., Hegde, R. S., and Taunton, J. (2005) A substrate-specific inhibitor of protein translocation into the endoplasmic reticulum Nature 436, 285-289
58. Besemer, J., Harant, H., Wang, S., Oberhauser, B., Marquardt, K., Foster, C. A., Schreiner, E. P., de Vries, J. E., Dascher-Nadel, C., and Lindley, I. J. (2005) Selective inhibition of cotranslational translocation of vascular cell adhesion molecule 1 Nature 436, 290-293
59. Klemm, J. D., Schreiber, S. L., and Crabtree, G. R. (1998) Dimerization as a regulatory mechanism in signal transduction Annu. Rev. Immunol. 16, 569-592
60. Okuzumi, T., Fiedler, D., Zhang, C., Gray, D. C., Aizenstein, B., Hoffman, R., and Shokat, K. M. (2009) Inhibitor hijacking of Akt activation Nat. Chem. Biol. 5, 484-493
61. Deribe, Y. L., Pawson, T., and Dikic, I. (2010) Post-translational modifications in signal integration Nat. Struct. Mol. Biol. 17, 666-672
62. Potashman, M. H. and Duggan, M. E. (2009) Covalent modifiers: an orthogonal approach to drug design J. Med. Chem. 52, 1231-1246
63. Ahn, Y. H., Hwang, Y., Liu, H., Wang, X. J., Zhang, Y., Stephenson, K. K., Boronina, T. N., Cole, R. N., Dinkova-Kostova, A. T., Talalay, P., and Cole, P. A. (2010) Electrophilic tuning of the chemoprotective natural product sulforaphane Proc. Natl. Acad. Sci. U.S.A. 107, 9590-9595
64. Cameron, A. J., Escribano, C., Saurin, A. T., Kostelecky, B., and Parker, P. J. (2009) PKC maturation is promoted by nucleotide pocket occupation independently of intrinsic kinase activity Nat. Struct. Mol. Biol. 16, 624-630
65. Erlanson, D. A., Braisted, A. C., Raphael, D. R., Randal, M., Stroud, R. M., Gordon, E. M., and Wells, J. A. (2000) Site-directed ligand discovery Proc. Natl. Acad. Sci. U.S.A. 97, 9367-9372
66. Scheer, J. M., Romanowski, M. J., and Wells, J. A. (2006) A common allosteric site and mechanism in caspases Proc. Natl. Acad. Sci. U.S.A. 103, 7595-7600
67. Coyne, A. G., Scott, D. E., and Abell, C. (2010) Drugging challenging targets using fragment-based approaches Curr. Opin. Chem. Biol. 14, 299-307
68. Murray, C. W. and Rees, D. C. (2009) The rise of fragment-based drug discovery Nat. Chem. 1, 187-192
69. Jahnke, W., Rondeau, J. M., Cotesta, S., Marzinzik, A., Pelle, X., Geiser, M., Strauss, A., Gotte, M., Bitsch, F., Hemmig, R., Henry, C., Lehmann, S., Glickman, J. F., Roddy, T. P., Stout, S. J., and Green, J. R. (2010) Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery Nat. Chem. Biol. 6, 660-666
70. 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., and Rosenberg, S. H. (2005) An inhibitor of Bcl-2 family proteins induces regression of solid tumours Nature 435, 677-681
71. Lockless, S. W. and Ranganathan, R. (1999) Evolutionarily conserved pathways of energetic connectivity in protein families Science 286, 295-299
72. Suel, G. M., Lockless, S. W., Wall, M. A., and Ranganathan, R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins Nat. Struct. Biol. 10, 59-69
73. Massova, I. and Mobashery, S. (1999) Structural and mechanistic aspects of evolution of beta-lactamases and penicillin-binding proteins Curr. Pharm. Des. 5, 929-937
74. Schuyler, A. D., Carlson, H. A., and Feldman, E. L. (2010) Computational methods for identifying a layered allosteric regulatory mechanism for ALS-causing mutations of Cu-Zn superoxide dismutase 1 Proteins 79, 417-427
75. Ota, N. and Agard, D. A. (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion J. Mol. Biol. 351, 345-354
76. Hendlich, M., Rippmann, F., and Barnickel, G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins J. Mol. Graph. Model. 15, 359-363, 389
77. Kalidas, Y. and Chandra, N. (2008) PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins J. Struct. Biol. 161, 31-42
78. Lexa, K. W. and Carlson, H. A. (2010) Full protein flexibility is essential for proper hot-spot mapping J. Am. Chem. Soc. 133, 200-202
79. Desai, A. and Mitchison, T. J. (1997) Microtubule polymerization dynamics Annu. Rev. Cell. Dev. Biol. 13, 83-117
80. Steitz, T. A. (2008) A structural understanding of the dynamic ribosome machine Nat. Rev. Mol. Cell. Biol. 9, 242-253
81. LaRiviere, F. J., Wolfson, A. D., and Uhlenbeck, O. C. (2001) Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation Science 294, 165-168
82. Schrader, J. M., Chapman, S. J., and Uhlenbeck, O. C. (2011) Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding Proc. Natl. Acad. Sci. U.S.A. 108, 5215-5220
83. Davydov, D. R., Rumfeldt, J. A., Sineva, E. V., Fernando, H., Davydova, N. Y., and Halpert, J. R. (2012)) Peripheral ligand-binding site in cytochrome P450 3A4 located with fluorescence resonance energy transfer (FRET) J. Biol. Chem. 287, 6797-6809
84. Bill, A., Blockus, H., Stumpfe, D., Bajorath, J., Schmitz, A., and Famulok, M. (2011) A homogeneous fluorescence resonance energy transfer system for monitoring the activation of a protein switch in real time J. Am. Chem. Soc. 133, 8372-8379
85. Coward, P., Conn, M., Tang, J., Xiong, F., Menjares, A., and Reagan, J. D. (2009) Application of an allosteric model to describe the interactions among retinol binding protein 4, transthyretin, and small molecule retinol binding protein 4 ligands Anal. Biochem. 384, 312-320
86. Soderholm, J. F., Bird, S. L., Kalab, P., Sampathkumar, Y., Hasegawa, K., Uehara-Bingen, M., Weis, K., and Heald, R. (2011) Importazole, a small molecule inhibitor of the transport receptor importin-beta ACS Chem. Biol. 6, 700-708
87. Cellitti, S. E., Jones, D. H., Lagpacan, L., Hao, X., Zhang, Q., Hu, H., Brittain, S. M., Brinker, A., Caldwell, J., Bursulaya, B., Spraggon, G., Brock, A., Ryu, Y., Uno, T., Schultz, P. G., and Geierstanger, B. H. (2008) In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy J. Am. Chem. Soc. 130, 9268-9281
88. Tugarinov, V. and Kay, L. E. (2005) Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins ChemBioChem 6, 1567-1577
89. Al-Hashimi, H. M. (2010) Biochemistry. Exciting structures Science 329, 1295-1296
90. Verma, R., Peters, N. R., D'Onofrio, M., Tochtrop, G. P., Sakamoto, K. M., Varadan, R., Zhang, M., Coffino, P., Fushman, D., Deshaies, R. J., and King, R. W. (2004) Ubistatins inhibit proteasome-dependent degradation by binding the ubiquitin chain Science 306, 117-120
91. Bobkova, E. V., Weber, M. J., Xu, Z., Zhang, Y. L., Jung, J., Blume-Jensen, P., Northrup, A., Kunapuli, P., Andersen, J. N., and Kariv, I. (2010) Discovery of PDK1 kinase inhibitors with a novel mechanism of action by ultrahigh throughput screening J. Biol. Chem. 285, 18838-18846
92. Converso, A., Hartingh, T., Garbaccio, R. M., Tasber, E., Rickert, K., Fraley, M. E., Yan, Y., Kreatsoulas, C., Stirdivant, S., Drakas, B., Walsh, E. S., Hamilton, K., Buser, C. A., Mao, X., Abrams, M. T., Beck, S. C., Tao, W., Lobell, R., Sepp-Lorenzino, L., Zugay-Murphy, J., Sardana, V., Munshi, S. K., Jezequel-Sur, S. M., Zuck, P. D., and Hartman, G. D. (2009) Development of thioquinazolinones, allosteric Chk1 kinase inhibitors Bioorg. Med. Chem. Lett. 19, 1240-1244
93. Erlbruch, A., Hung, C. W., Seidler, J., Borrmann, K., Gesellchen, F., Konig, N., Kubler, D., Herberg, F. W., Lehmann, W. D., and Bossemeyer, D. (2010) Uncoupling of bait-protein expression from the prey protein environment adds versatility for cell and tissue interaction proteomics and reveals a complex of CARP-1 and the PKA Cbeta1 subunit Proteomics 10, 2890-2900
94. Moulick, K., Ahn, J. H., Zong, H., Rodina, A., Cerchietti, L., Gomes DaGama, E. M., Caldas-Lopes, E., Beebe, K., Perna, F., Hatzi, K., Vu, L. P., Zhao, X., Zatorska, D., Taldone, T., Smith-Jones, P., Alpaugh, M., Gross, S. S., Pillarsetty, N., Ku, T., Lewis, J. S., Larson, S. M., Levine, R., Erdjument-Bromage, H., Guzman, M. L., Nimer, S. D., Melnick, A., Neckers, L., and Chiosis, G. (2011) Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90 Nat. Chem. Biol. 7, 818-826
95. Deacon, S. W., Beeser, A., Fukui, J. A., Rennefahrt, U. E., Myers, C., Chernoff, J., and Peterson, J. R. (2008) An isoform-selective, small-molecule inhibitor targets the autoregulatory mechanism of p21-activated kinase Chem. Biol. 15, 322-331
96. Miyata, Y., Chang, L., Bainor, A., McQuade, T. J., Walczak, C. P., Zhang, Y., Larsen, M. J., Kirchhoff, P., and Gestwicki, J. E. (2010) High-throughput screen for Escherichia coli heat shock protein 70 (Hsp70/DnaK): ATPase assay in low volume by exploiting energy transfer J. Biomol. Screening 15, 1211-1219
97. Wisen, S., Bertelsen, E. B., Thompson, A. D., Patury, S., Ung, P., Chang, L., Evans, C. G., Walter, G. M., Wipf, P., Carlson, H. A., Brodsky, J. L., Zuiderweg, E. R., and Gestwicki, J. E. (2010) Binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40 ACS Chem. Biol. 5, 611-622
98. Berggard, T., Linse, S., and James, P. (2007) Methods for the detection and analysis of protein-protein interactions Proteomics 7, 2833-2842
99. Perkins, J. R., Diboun, I., Dessailly, B. H., Lees, J. G., and Orengo, C. (2010) Transient protein-protein interactions: structural, functional, and network properties Structure 18, 1233-1243
100. Kerppola, T. K. (2008) Bimolecular fluorescence complementation (BiFC) analysis as a probe of protein interactions in living cells Annu. Rev. Biophys. 37, 465-487
101. Krishnamurthy, M., Dugan, A., Nwokoye, A., Fung, Y. H., Lancia, J. K., Majmudar, C. Y., and Mapp, A. K. (2011) Caught in the act: covalent cross-linking captures activator-coactivator interactions in vivo ACS Chem. Biol. 6, 1321-1326
102. Pellegrini, M. (2003) Defining interacting partners for drug discovery Expert Opin. Ther. Targets 7, 287-297
103. Tanaka, Y., Bond, M. R., and Kohler, J. J. (2008) Photocrosslinkers illuminate interactions in living cells Mol. Biosyst. 4, 473-480
104. Majmudar, C. Y., Lee, L. W., Lancia, J. K., Nwokoye, A., Wang, Q., Wands, A. M., Wang, L., and Mapp, A. K. (2009) Impact of nonnatural amino acid mutagenesis on the in vivo function and binding modes of a transcriptional activator J. Am. Chem. Soc. 131, 14240-14242
105. Clark, M. A. (2010) Selecting chemicals: the emerging utility of DNA-encoded libraries Curr. Opin. Chem. Biol. 14, 396-403
106. Dandapani, S. and Marcaurelle, L. A. (2010) Grand challenge commentary: Accessing new chemical space for 'undruggable' targets Nat. Chem. Biol. 6, 861-863
107. Dandapani, S. and Marcaurelle, L. A. (2010) Current strategies for diversity-oriented synthesis Curr. Opin. Chem. Biol. 14, 362-370
108. Goldman, S. (2010) Genetic Chemistry: Production of non-native compounds in yeast Curr. Opin. Chem. Biol. 14, 390-395
109. Gestwicki, J. E., Crabtree, G. R., and Graef, I. A. (2004) Harnessing chaperones to generate small-molecule inhibitors of amyloid beta aggregation Science 306, 865-869
110. Fletcher, S. and Hamilton, A. D. (2005) Protein surface recognition and proteomimetics: mimics of protein surface structure and function Curr. Opin. Chem. Biol. 9, 632-638
111. Buerger, C. and Groner, B. (2003) Bifunctional recombinant proteins in cancer therapy: cell penetrating peptide aptamers as inhibitors of growth factor signaling J. Cancer Res. Clin. Oncol. 129, 669-675
112. Traczewski, P. and Rudnicka, L. (2011) Treatment of systemic lupus erythematosus with epratuzumab Br. J. Clin. Pharmacol. 71, 175-182
113. Drewry, D. H. and Macarron, R. (2010) Enhancements of screening collections to address areas of unmet medical need: an industry perspective Curr. Opin. Chem. Biol. 14, 289-298
114. Renner, S., Popov, M., Schuffenhauer, A., Roth, H. J., Breitenstein, W., Marzinzik, A., Lewis, I., Krastel, P., Nigsch, F., Jenkins, J., and Jacoby, E. (2011) Recent trends and observations in the design of high-quality screening collections Future Med. Chem. 3, 751-766
115. Wang, R., Fang, X., Lu, Y., and Wang, S. (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures J. Med. Chem. 47, 2977-2980
116. Negi, S. S., Schein, C. H., Oezguen, N., Power, T. D., and Braun, W. (2007) InterProSurf: a web server for predicting interacting sites on protein surfaces Bioinformatics 23, 3397-3399