Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface

PLoS Computational Biology

Volumn 9, Issue 3, 2013, Pages

  Johnson, David K ^a   Karanicolas, John ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG INTERACTIONS; LIGANDS; MOLECULES; PROTEINS;

HIGH THROUGHPUT SCREENING; MODELLING SYSTEMS; PROTEIN FLUCTUATIONS; PROTEIN INTERACTION; PROTEIN INTERACTION SITES; PROTEIN SURFACE; PROTEIN-PROTEIN INTERACTIONS; PROTEINS STRUCTURES; SMALL MOLECULES; SMALL-MOLECULE BINDINGS;

CONFORMATIONS;

SURVIVIN;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

EID: 84875984520     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002951     Document Type: Article

References (50)

1. Sun H, Stuckey JA, Nikolovska-Coleska Z, Qin D, Meagher JL, et al. (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.
2. Bruncko M, Oost TK, Belli BA, Ding H, Joseph MK, et al. (2007) Studies leading to potent, dual inhibitors of Bcl-2 and Bcl-xL. J Med Chem 50: 641-662.
3. Rush TS 3rd, Grant JA, Mosyak L, Nicholls A, (2005) A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. Journal of medicinal chemistry 48: 1489-1495.
4. Wang Y, Coulombe R, Cameron DR, Thauvette L, Massariol MJ, et al. (2004) Crystal structure of the E2 transactivation domain of human papillomavirus type 11 bound to a protein interaction inhibitor. J Biol Chem 279: 6976-6985.
5. Thanos CD, Randal M, Wells JA, (2003) Potent small-molecule binding to a dynamic hot spot on IL-2. J Am Chem Soc 125: 15280-15281.
6. Becker JW, Rotonda J, Cryan JG, Martin M, Parsons WH, et al. (1999) 32-Indolyl ether derivatives of ascomycin: three-dimensional structures of complexes with FK506-binding protein. J Med Chem 42: 2798-2804.
7. Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, et al. (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303: 844-848.
8. Wells JA, McClendon CL, (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450: 1001-1009.
9. Alsmadi O, Herz R, Murphy E, Pinter A, Tilley SA, (1997) A novel antibody-dependent cellular cytotoxicity epitope in gp120 is identified by two monoclonal antibodies isolated from a long-term survivor of human immunodeficiency virus type 1 infection. J Virol 71: 925-933.
10. Domling A, (2008) Small molecular weight protein-protein interaction antagonists: an insurmountable challenge? Curr Opin Chem Biol 12: 281-291.
11. Rechfeld F, Gruber P, Hofmann J, Kirchmair J, (2011) Modulators of protein-protein interactions: novel approaches in targeting protein kinases and other pharmaceutically relevant biomolecules. Curr Top Med Chem 11: 1305-1319.
12. Zinzalla G, Thurston DE, (2009) Targeting protein-protein interactions for therapeutic intervention: a challenge for the future. Future Med Chem 1: 65-93.
13. Kenny CH, Ding W, Kelleher K, Benard S, Dushin EG, et al. (2003) Development of a fluorescence polarization assay to screen for inhibitors of the FtsZ/ZipA interaction. Anal Biochem 323: 224-233.
14. Hajduk PJ, Huth JR, Fesik SW, (2005) Druggability indices for protein targets derived from NMR-based screening data. Journal of medicinal chemistry 48: 2518-2525.
15. Mattos C, Bellamacina CR, Peisach E, Pereira A, Vitkup D, et al. (2006) Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol 357: 1471-1482.
16. Metz A, Pfleger C, Kopitz H, Pfeiffer-Marek S, Baringhaus KH, et al. (2012) Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J Chem Inf Model 52: 120-133.
17. Seco J, Luque FJ, Barril X, (2009) Binding site detection and druggability index from first principles. Journal of medicinal chemistry 52: 2363-2371.
18. Eyrisch S, Helms V, (2007) Transient pockets on protein surfaces involved in protein-protein interaction. J Med Chem 50: 3457-3464.
19. Laurie AT, Jackson RM, (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916.
20. Foster TJ, MacKerell AD Jr, Guvench O, (2012) Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. Journal of computational chemistry 33: 1880-1891.
21. Clodfelter KH, Waxman DJ, Vajda S, (2006) Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450. Biochemistry 45: 9393-9407.
22. Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, et al. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chemical biology & drug design 71: 106-116.
23. Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S, (2007) Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. Journal of medicinal chemistry 50: 1231-1240.
24. Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ, (2007) Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs. Biochemistry 46: 2640-2654.
25. Eyrisch S, Helms V, (2009) What induces pocket openings on protein surface patches involved in protein-protein interactions? J Comput Aided Mol Des 23: 73-86.
26. Bakan A, Nevins N, Lakdawala AS, Bahar I, (2012) Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. Journal of chemical theory and computation 8: 2435-2447.
27. Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, et al. (2011) Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci U S A 108: 13528-13533.
28. Huang B, Schroeder M, (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC structural biology 6: 19.
29. Brady GP Jr, Stouten PF, (2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 14: 383-401.
30. Hendlich M, Rippmann F, Barnickel G, (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. Journal of Molecular Graphics & Modelling 15: 359-389, 359-363, 389.
31. Liang J, Edelsbrunner H, Woodward C, (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 7: 1884-1897.
32. Peters KP, Fauck J, Frommel C, (1996) The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J Mol Biol 256: 201-213.
33. Weisel M, Proschak E, Schneider G, (2007) PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem Cent J 1: 7.
34. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-574.
35. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, et al. (1999) Analysis of human transcriptomes. Nat Genet 23: 387-388.
36. Paik S, Shak S, Tang G, Kim C, Baker J, et al. (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351: 2817-2826.
37. Rodel F, Frey B, Leitmann W, Capalbo G, Weiss C, et al. (2008) Survivin antisense oligonucleotides effectively radiosensitize colorectal cancer cells in both tissue culture and murine xenograft models. Int J Radiat Oncol Biol Phys 71: 247-255.
38. Lewis KD, Samlowski W, Ward J, Catlett J, Cranmer L, et al. (2011) A multi-center phase II evaluation of the small molecule survivin suppressor YM155 in patients with unresectable stage III or IV melanoma. Invest New Drugs 29: 161-166.
39. Kita A, Nakahara T, Yamanaka K, Nakano K, Nakata M, et al. (2011) Antitumor effects of YM155, a novel survivin suppressant, against human aggressive non-Hodgkin lymphoma. Leukemia research 35: 787-792.
40. Altieri DC, (2008) Survivin, cancer networks and pathway-directed drug discovery. Nature reviews Cancer 8: 61-70.
41. Sun H, Lu J, Liu L, Yi H, Qiu S, et al. (2010) Nonpeptidic and potent small-molecule inhibitors of cIAP-1/2 and XIAP proteins. J Med Chem 53: 6361-6367.
42. Dean EJ, Ward T, Pinilla C, Houghten R, Welsh K, et al. (2010) A small molecule inhibitor of XIAP induces apoptosis and synergises with vinorelbine and cisplatin in NSCLC. Br J Cancer 102: 97-103.
43. Wang Z, Cuddy M, Samuel T, Welsh K, Schimmer A, et al. (2004) Cellular, biochemical, and genetic analysis of mechanism of small molecule IAP inhibitors. J Biol Chem 279: 48168-48176.
44. Schimmer AD, Welsh K, Pinilla C, Wang Z, Krajewska M, et al. (2004) Small-molecule antagonists of apoptosis suppressor XIAP exhibit broad antitumor activity. Cancer Cell 5: 25-35.
45. Wendt MD, Sun C, Kunzer A, Sauer D, Sarris K, et al. (2007) Discovery of a novel small molecule binding site of human survivin. Bioorg Med Chem Lett 17: 3122-3129.
46. Cheng AC, Coleman RG, Smyth KT, Cao Q, Soulard P, et al. (2007) Structure-based maximal affinity model predicts small-molecule druggability. Nature Biotechnology 25: 71-75.
47. Koes D, Khoury K, Huang Y, Wang W, Bista M, et al. (2012) Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One 7: e32839.
48. Quintus F, Sperandio O, Grynberg J, Petitjean M, Tuffery P, (2009) Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. BMC Bioinformatics 10: 245.
49. Shuker SB, Hajduk PJ, Meadows RP, Fesik SW, (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274: 1531-1534.
50. Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264.