Nichtkompetitive Inhibition der tRNA-Guanin Transglycosylase durch Störung der essentiellen Protein-Protein-Interaktion

Protein-Protein-Kontakte stellen eine reiche Vielfalt an Interaktionsmöglichkeiten der Polypeptide mit regulatorischen Funktionen innerhalb lebender Organismen dar. Das homodimere Enzym tRNA-Guanin Transglykosylase(TGT) katalysiert z. B. eine Basenaustauschreaktion, die essentiell für die Pathogeni...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
1. Verfasser: Jakobi, Stephan
Beteiligte: Klebe, Gerhard (Prof. Dr.) (BetreuerIn (Doktorarbeit))
Format: Dissertation
Veröffentlicht: Philipps-Universität Marburg 2013
Pharmazeutische Chemie
Online Zugang:PDF-Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!



3. J. Janin, Protein-Protein Complexes Analysis, Modeling and Drug Design., Imperial College Press, 2010, Kap. X-ray Study of Protein-Protein Complexes and Analysis of Interfaces, 1.

4. J. Wang, R. Wolf, J. Caldwell, P. Kollman, D. Case, Development and testing of a general Amber force field, J. Comput. Chem. 2004, 25, 1157.

5. J. Izaguirre, D. Catarello, J. Wozniak, R. Skeel, Langevin stabilization of molecular dynamics, J. Chem. Phys. 2001, 114, 2090.

6. G. Schröder, H. Hilbi, Molecular Pathogenesis of Shigella spp.: Controlling Host Cell Signaling, Invasion, and Death by Type III Secretion, Clin. Microbiol. Rev. 2008, 21, 134.

7. H. Ponstingl, K. Hendrick, J. Thornton, Discriminating Between Ho- modimeric and Monomeric Proteins in the Crystalline State, Proteins: Struct., Funct., Bioinf. 2000, 41, 47.

8. B. Stengl, K. Reuter, G. Klebe, Mechanism and Substrate Specifity of tRNA-Guanine Transglycosylases (TGTs): tRNA-Modifying Enzymes from the Three Different Kingdoms of Life Share a Common Catylytic Mechanism, Chem- BioChem 2005, 6, 1926.

9. T. Ritschel, P. C. Kohler, G. Neudert, A. Heine, F. Diederich, G. Kle- be, How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase, ChemMed- Chem 2009, 4, 2012.

10. P. Buchwald, Small-Molecule Protein-Protein Interaction Inhibitors: Thera- peutic Potential in Light of Molecular Size, Chemical Space, and Ligand Binding Efficiency Considerations, IUBMB Life 2010, 62, 724.

11. H. Gohlke, D. A. Case, Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf, J. Comput. Chem. 2004, 25, 238.

12. S. Huo, I. Massova, P. A. Kollman, Computational Alanine Scanning of the 1:1 Human Growth Hormone-Receptor Complex, J. Comput. Chem. 2002, 23, 15.

13. M. Abu-Farha, F. Elisma, D. Figeys, Identifacation of Protein-Protein Interactions by Mass Spectrometry Coupled Techniques, Adv. Biochem. Eng./Biotechnol. 2008, 110, 67.

14. S. Sanglier, C. Atmanene, G. Chevreux, A. van Dorsselaer, Nonde- naturing Mass Spectrometry to Study Noncovalent Protein/Protein and Prote- in/Ligand Complexes: Technical Aspects and Application to the Determination of Binding Stoichiometries, in Methods in Molecular Biology, vol. 484: Functional Proteomics: Methods and Protocols, 2009, 217.

15. A. Téllez-Valencia, V. Olivares-Illana, A. Hernández-Santoyo, R. Pérez-Montfort, M. Costas, A. Rodríguez-Romero, F. López- Calahorra, M. de Gómez-Puyou, A. Gómez-Puyou, Inactivation of Trio- sephaosphate Isomerase from Trypanosoma cruzi by an Agent that Perturbs its Dimer Interface, J. Mol. Biol. 2004, 341, 1355.

16. C. Romier, J. Meyer, D. Suck, Slight sequence variations of a common fold explain the substrate specificities of tRNA-guanine transglycosylases from the three kingdoms, FEBS Lett. 1997, 416, 93.

17. L. Bannwarth, T. Rose, L. Dufau, R. Vanderesse, J. Dumond, B. Jamart-Grégoire, C. Pannecouque, E. De Clercq, M. Reboud- Ravaux, Dimer Disruption and Monomer Sequestration by Alkyl Tripeptides are Sucsessful Strategies for Inhibiting Wild-Type and Multidrug-Resistant Mutated HIV-1 Proteases, Biochemistry 2009, 48, 379.

18. R. Brenk, L. Naerum, U. Grädler, H.-D. Gerber, G. A. Garcia, K. Reuter, M. T. Stubbs, G. Klebe, Virtual Screening for Submicromolar Leads of tRNA-guanine Transglycosylase Based on a New Unexpected Binding Mode Detected by Crystal Structure Analysis, J. Med. Chem. 2003, 46, 1133.

19. A. Orcajo-Rincón, S. Ortega-Gutiérrez, P. Serrano, I. Torrecillas, K. Wüthrich, M. Campillo, L. Pardo, A. Viso, B. Benhamú, M. López- Rodríguez, Development of Non-Peptide Ligands of Growth Factor Receptor- Bound Protein 2-Src Homology 2 Domain Using Molecular Modeling and NMR Spectroscopy, J. Med. Chem. 2011, 54, 1096.

20. J. Seco, F. J. Luque, X. Barril, Binding Site Detection and Druggability Index from First Principles, J. Med. Chem. 2009, 52, 2363.

21. W. Xie, X. Liu, R. H. Huang, Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate, Nat. Struct. Biol. 2003, 10, 781.

22. L. Espinoza-Fonseca, Aromatic residues link binding and function of intrinsi- cally disordered proteins, Mol. BioSyst. 2012, 8, 237.

23. Jones, J. Thornton, Principles of protein-protein interactions, Proc. Natl. Acad. Sci. USA 1996, 93, 13.

24. N. Kannan, S. Vishveshwara, Aromatic clusters: a determinant of thermal stability of thermophilic proteins, Protein Eng., Des. Sel. 2000, 13, 753.

25. Y.-C. Chen, V. P. Kelly, S. V. Stachura, G. A. Garcia, Characterization of the human tRNA-guanine transglycosylase: Confirmation of the heterodimeric subunit structure, RNA 2010, 16, 958.

26. N. Kannan, S. Vishveshwara, Identification of side-chain clusters in protein structures by a graph spectral method, J. Mol. Biol. 1999, 292, 441.

27. D. Cardinale, O. Salo-Ahen, S. Ferrari, G. Ponterini, G. Cruciani, E. Carosati, A. Tochowicz, S. Mangani, R. Wade, M. Costi, Homodi- meric Enzymes as Drug Targets, Curr. Med. Chem. 2010, 17, 826.

28. H. Alonso, A. Bliznyuk, J. Gready, Combining Docking and Molecular Dynamic Simulations in Drug Design, Med. Res. Rev. 2006, 26, 531.

29. H. Guan, E. Kiss-Toth, Advanced Technologies for Studies on Protein Inter- actoms, Adv. Biochem. Eng./Biotechnol. 2008, 110, 1.

30. E. Gasteiger, C. Hoogland, A. Gattker, S. Duvaud, M. Wilkins, R. Appel, A. Bairoch, Protein Identifikation and Analysis Tool on the ExPASy Server, in J. Walker (Hg.), The Proteomics Protocols Handbook, Humana Press, 2005, 571.

31. N. Kresge, V. Vacquir, C. Stout, Abalone Lysin: The dissolving and evolving sperm protein., Bioessays 2001, 23, 95.

32. H. Sassmannshausen, A CAII case study with tethered ligands: Docking with water, fail-safe or flawed?, Diplomarbeit, Philipps-Universität Marburg, 2010.

33. T. Clackson, J. A. Wells, A Hot Spot of Binding Energy in a Hormone- Receptor Interface, Science 1995, 267, 383.

34. T. Ritschel, C. Atmanene, K. Reuter, A. van Dorsselaer, S. Sangler- Cianferani, G. Klebe, An Integrative Approach Combining Noncovalent Mass Spectrometry, Enzyme Kinetics and X-ray Crystallography to Decipher Tgt Protein-Protein and Protein-RNA Interaction, J. Mol. Biol. 2009, 393, 833.

35. S. Burley, G. Petsko, Aromatic-Aromatic Interaction: A Mechanism of Protein Structure Stabilization, Science 1985, 229, 23.

36. Oslob, D. R. Raphael, L. Taylor, J. Wang, R. S. McDowell, J. A. Wells, A. C. Braisted, Binding of small molecules to an adaptive protein- protein interface, Proc. Natl. Acad. Sci. USA 2003, 100, 1603.

37. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmer- ling, Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters, Proteins: Struct., Funct., Bioinf. 2006, 65, 712.

38. D. Grimme, D. González-Ruiz, H. Gohlke, Computational Strategies and Challenges for Targeting Protein-Protein Interactions with Small Molecules, in J. Luque, X. Barril (Hg.), RSC Drug Discovery Series No. 23: Physico- Chemical and Computational Approaches to Drug Discovery, Royal Society of Chemistry, 2012, 319.

39. R. Brenk, E. A. Meyer, K. Reuter, M. T. Stubbs, G. A. Garcia, F. Diederich, G. Klebe, Crystallographic Study of Inhibitors of tRNA-guanine Transglycosylase Suggests a New Structure-based Pharmacophore for Virtual Screening, J. Mol. Biol. 2004, 338, 55.

40. C. Romier, K. Reuter, D. Suck, R. Ficner, Crystal structure of tRNA- guanine transglycosylase: RNA modification by base exchange, EMBO J. 1996, 15, 2850.

41. B. Stengl, E. A. Meyer, A. Heine, R. Brenk, F. Diederich, G. Klebe, Crystal Structures of tRNA-guanine Transglycosylase (TGT) in Complex with Novel and Potent Inhibitors Unravel Pronounced Induced-fit Adaptations and Suggests Dimer Formation Upon Substrate Binding, J. Mol. Biol. 2007, 370, 492.

42. U. Grädler, De Novo-Design und Strukturbestimmung von Inhibitoren der tRNA-Guanin Transglykosylase aus Zymomonas mobilis als neues Target der Bakterienruhr, Dissertation, Philipps-Universität Marburg, 2000.

43. T. Adam, Die Invasion von Epithelzellen durch E. coli Shigella, Dissertation, Medizinische Fakultät der Charité -Universitätsmedizin Berlin, 2003.

44. D. Erlanson, R. S. McDowell, M. M. He, M. Randal, R. L. Simmons, J. Kung, A. Waight, S. K. Hansen, Discovery of a New Phosphotyrosine Mimetic for PTP1B Using Breakaway Tethering, J. Am. Chem. Soc. 2003, 125, 5602.

45. A. Pretros, J. Dinges, D. Augeri, S. Baumeister, D. Betebenner, M. Bures, S. Elmore, P. Hajduk, M. Joseph, S. Landis, D. Nettesheim, W. Rosenberg, S.H. Shen, S. Thomas, X. Wang, I. Zanze, H. Zhang, S. Fesik, Discovery of a Potent Inhibitor of the Antiapoptotic Protein Bcl-xL from NMR and Parallel Synthesis, J. Med. Chem. 2006, 49, 656.

46. G. Neudert, G. Klebe, DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes, J. Chem. Inf. Model. 2011, 51, 2731.

47. IBA GmbH, Expression and purification of proteins using Strep-tag and/or 6xHistidine-tag. A comprehensive manual., 2011.

48. A. Jakalian, B. Bush, D. Jack, C. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method, J. Comput. Chem. 2000, 21, 132.

49. G. Neudert, G. Klebe, fconv: Format conversion, manipulation and feature computation of molecular data, Bioinformatics 2011, 7, 1021.

50. G. Chessari, A. Woodhead, From fragment to clinical candidate -a historical perspective, Drug Discovery Today 2009, 14, 668.

51. T. Hale, Genetic Bais of Virulence in Shigella Species, Microbiol. Mol. Biol. Rev. 1991, 55, 206.

52. Swerdlow, P. J. Sansonetti, G. K. Adak, M. M. Levine, Global burden of Shigella infections: implications for vaccine development and implementation of control strategies, Bulletin of the World Health Organization 1999, 77, 651.

53. I. S. Moreira, P. A. Fernandes, M. J. Ramos, Hot spots -A review of the protein-protein interface determinant amino-acid residues, Proteins: Struct., Funct., Bioinf. 2007, 68, 803.

54. E. Krissinel, K. Henrick, Inference of macromolecular assemblies from cry- stalline state, J. Mol. Biol. 2007, 372, 774.

55. H. Gohlke, C. Kiel, D. A. Case, Insights into Protein-Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes, J. Mol. Biol. 2003, 330, 891.

56. F. Immekus, lin -Benzopurines as Inhibitors of tRNA-Guanine Transglyco- sylase: Perturbance of Homodimer Formation, Import of Water Clusters and Determinants of Crystallographical Disorder, Dissertation, Philipps-Universität Marburg, 2013.

57. T. Berg, Modulation von Protein-Protein-Wechselwirkungen mit niedermoleku- laren organischen Molekülen, Angew. Chem. 2003, 115, 2566.

58. J.-P. Ryckaert, G. Ciccotti, H. Berendsen, Numerical integration of the cartesian equation of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 1977, 23, 327.

59. J. Martinez, L. Martinez, Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking, J. Comput. Chem. 2002, 24, 819. XXXVII G Literaturverzeichnis [85] L. Martinez, R. Andrade, E. Birgin, J. Martinez, Packmol: A package for building initial configurations for molecular dynamics simulations, J. Comput. Chem. 2009, 30, 2157.

60. T. Darden, D. York, L. Pedersen, Particle mesh Ewald: an N · log(N ) method for Ewald sums in large systems., J. Chem. Phys. 1993, 98, 10089.

61. J. Fuller, N. Burgoyne, R. Jackson, Predicting druggable binding sites at the protein-protein interface, Drug Discovery Today 2009, 14, 155. XXXIII G Literaturverzeichnis [47] S. Assi, T. Tanaka, T. Rabbitts, N. Fernandez-Fuentes, PCRPi: Presa- ging Critical Residues in Protein interfaces, a new computational toll to chart hot spots in protein interfaces, Nucleic Acids Res. 2010, 38, e86.

62. Z. Otwinowski, W. Minor, Processing of X-ray Diffraction Data Collected in Oscillation Mode, Methods in Enzymology 1997, 276, 307.

63. G. McGaughey, M. Gagné, A. Rappeé, π-Stacking Interactions. Alive and well in Proteins., J. Biol. Chem. 1998, 273, 15458.

64. K. Reuter, R. Ficner, Sequence Analysis and Overexpresson of the Zymomo- nas mobilis tgt Gene Encoding tRNA-Guanin Transglycosylase: Purification and Biochemical Characterization of the Enzyme, J. Bacteriol. 1995, 177, 5284.

65. M. Arkin, J. Wells, Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing towards the Dream, Nat. Rev. Drug Discovery 2004, 3, 301.

66. F. Terwesten, Studien zur fragmentbasierten Leitstrukturidentifizierung eines TGT-Interface-Inhibitors, Diplomarbeit, Philipps-Universität Marburg, 2011.

67. Y.-P. Pang, K. Xu, J. El Yazal, F. G. Prendergast, Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach, Protein Sci. 2000, 9, 1857.

68. C. Romier, R. Ficner, K. Reuter, D. Suck, Purification, Crystallization, and Perliminary X-Ray Diffraction Studies of tRNA-Guanin Transglycosylase From Zymomonas mobilis, Proteins: Struct., Funct., Bioinf. 1996, 24, 516.

69. G. Zinzalla, D. Thurston, Targeting protein-protein interactions for the- rapeutic intervention: a challenge for the future, Future Med. Chem. 2009, 1, 65. XXIX G Literaturverzeichnis

70. T. Ritschel, TGT a Drug Target to Study pKa Shifts, Residual Solvation & Protein -Protein Interface Formation, Dissertation, Philipps-Universität Marburg, 2009.

71. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, P. Bourne, The Protein Data Bank, Nucleic Acids Res. 2000, 28, 235.

72. The PyMOL Molecular Graphics System, Version 1.2, Schrödinger, LLC.

73. A. W. Curnow, F.-L. Kung, K. A. Koch, G. A. Garcia, tRNA-Guanine Transglycosylase from Escherichia coli: Gross tRNA Structural Requirements for Recognition, Biochemistry 1993, 32, 5239.

74. W. H. Organization, Vaccine Research and Development -New strategies for accelerating Shigella vaccine development, Weekly Epidemiological Record 1997, 72, 73.

75. G. Klebe, Virtual ligand screening: strategies, perspectives and limitations, Drug Discovery Today 2006, 11, 580.

76. J. Weiser, P. Shenkin, W. Still, Approximate Atomic Surfaces from Linear Combinations of Pairwise Overlaps (LCPO), J. Comput. Chem. 1999, 20, 217.

77. S. Dasgupta, G. Iyer, S. Bryant, C. Lawrence, J. Bell, Extent and Nature of Contacts Between Protein Molecules in Crystal Lattices and Between Subunits of Protein Oligomers, Proteins: Struct., Funct., Bioinf. 1997, 28, 494.

78. A. Onufriev, D. Bashford, D. Case, Exploring protein native states and large-scale conformational changes witha modified generalized Born model, Pro- teins: Struct., Funct., Bioinf. 2004, 55, 383.

79. J. Hoskins, S. Lovell, T. Blundell, An algorithm for predicting protein- protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements, Protein Sci. 2006, 15, 1017.

80. P. Mukherjee, P. Desai, Y.-D. Zhou, M. Avery, Targeting the BH3 Domain Mediated Protein-Protein Interaction of Bcl-xL through Virtual Screening, J. Chem. Inf. Model. 2010, 50, 906.

81. H. Köster, T. Craan, S. Brass, C. Herhaus, M. Zentgraf, L. Neumann, A. Heine, G. Klebe, A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes, J. Med. Chem. 2011, 54, 7784.

82. R. Bhattacharyya, U. Samanta, P. Chakrabarti, Aromatic-aromatic interactions in and around α-helices, Protein Eng., Des. Sel. 2002, 15, 91.

83. W. Jorgensen, J. Chandrasekhar, J. Madura, M. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 1983, 79, 926.

84. A. McCoy, R. Grosse-Kunstleve, P. Adams, M. Winn, L. Storoni, R. Read, Phaser crystallographic software, J. Appl. Crystallogr. 2007, 40, 658.

85. M. Winn, C. Ballard, K. Cowtan, E. Dodson, P. Emsley, P. Evans, R. Keegan, E. Krissinel, A. Leslie, A. McCoy, S. McNicholas, G. Murshudov, N. Pannu, E. Potterton, H. Powell, R. Read, A. Va- gin, K. Wilson, Overview of the CCP4 suite and current developments, Acta Crystallogr., Sect D: Biol. Crystallogr. 2011, 67, 235.

86. Q. Liu, J. Li, Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective, BMC Bioinformatics 2010, 11, 244.

87. M. Wendt, Protein-Protein Interactions as Drug Targets, in M. Wendt (Hg.), Topics in Medicinal Chemistry, 2012, Bd. 8, 1.

88. F. Immekus, L. Barandun, M. Betz, F. Debaene, S. Petiot, S. Sanglier- Cianferani, K. Reuter, F. Diederich, G. Klebe, Launching Spiking Ligands into a Protein-Protein Interface: A Promising Strategy to Destabilize and Break Interface Formation in a tRNA Modifying Enzyme, submitted.

89. P. Adams, P. Afonine, G. Bunkóczi, V. Chen, I. Davis, N. Echoo Is, J. Headd, L.-W. Hung, G. Kapral, R. Grosse-Kunstleve, A. McCoy, N. Moriarty, R. Oeffner, R. Read, D. Richardson, J. Richardson, T. Terwilliger, P. Zwart, PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr., Sect D: Biol. Crystallogr. 2010, 66, 213.

90. J. Wells, C. McClendon, Reaching for high-hanging fruit in drug discouvery at protein-protein interfaces, Nature 2007, 450, 1001.

91. I. Nooren, J. Thornton, Diversity of protein-protein-interactions, EMBO J. 2003, 22, 3486.

92. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, The Amber Biomolecular Simulation Programs, J. Comput. Chem. 2005, 26, 1668.

93. C.-J. Tsai, R. Nussinov, Hydrophobic folding units at protein-protein interfa- ces: Implications to protein folding and to protein-protein association, Protein Sci. 1997, 6, 1426.

94. C. Boland, P. Hayes, I. Santa-Maria, S. Nishimura, V. P. Kelly, Queuosine Formation in Eukaryotic tRNA Occurs via a Mitochondria-localized Heteromeric Transglycosylase, J. Biol. Chem. 2009, 284, 18218.

95. Dunker, S. O. Meroueh, Exploring the Molecular Design of Protein Interac- tion Sites with Molecular Dynamics Simulations and Free Energy Calculations, Biochemistry 2009, 48, 399.

96. XXXII G Literaturverzeichnis [38] A. Hanlon, M. Larkin, R. Reddick, Free-Solution, Label-Free Protein- Protein Interactions characterized by Dynamic Light Scattering, Biophys. J. 2010, 98, 297.

97. R. Bourgeas, M.-J. Basse, X. Morelli, P. Roche, Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database, PLoS One 2010, 5, 9598.

98. XXXVIII G Literaturverzeichnis [94] P. Emsley, B. Lohkam, W. Scott, K. Cowtan, Features and development of Coot, Acta Crystallogr., Sect D: Biol. Crystallogr. 2010, 66, 486.

99. K. Dill, K. Fiebig, H. Chan, Cooperativity in protein-folding kinetics, Proc. Natl. Acad. Sci. USA 1993, 90, 1942.

100. D. A. Pearlman, D. A. Case, J. Caldwell, W. S. Ross, T. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comput. Phys. Commun. 1995, 91, 1.

101. P. Fleming, F. Richards, Protein Packing: Dependence on Protein Size, Secondary Structure and Amino Acid Composition, J. Mol. Biol. 2000, 299, 487.

102. U. Grädler, H.-D. Gerber, D. M. Goodenoough-Lashua, G. A. Garcia, R. Ficner, K. Reuter, M. T. Stubbs, G. Klebe, A New Target for Shigello- sis: Rational Design and Crystallographic Studies of Inhibitors of tRNA-guanine Transglycosylase, J. Mol. Biol. 2001, 306, 455.

103. [28] A. A. Bogan, K. S. Thorn, Anatomy of Hot Spots in Protein Interfaces, J. Mol. Biol. 1998, 280, 1.

104. Raimundo, J. W. Lam, M. M. Sopko, H. E. Purkey, M. J. Romanowski, Tethering identifies fragment that yields potent inhibitors of human caspase-1, Bioorg. Med. Chem. Lett. 2006, 16, 559.

105. C. Joce, J. Stahl, M. Shridhar, M. Hutchinson, L. Watkins, P. Fe- dichev, H. Yin, Application of a novel in silico high-throughput screen to identify slective inhibitors for protein-protein interactions, Bioorg. Med. Chem. Lett. 2010, 20, 5411.

106. N. J. Marianayagam, M. Sunde, J. M. Matthews, The power of two: protein dimerization in biology, Trends Biochem. Sci. 2004, 29, 618.

107. M. Arkin, Protein-protein interactions and cancer: small molecules going in for the kill, Curr. Opin. Chem. Biol. 2005, 9, 315.

108. I. Moreira, J. Martins, R. Ramos, P. A. Fernandes, M. J. Ramos, Understanding the importance of the aromatic amino-acid residues as hot-spots, Biochim. Biophys. Acta 2013, 1834, 404.

109. Y. Tsuchiya, H. Nakamura, K. Kinoshita, Discrimination between biological interfaces and crystal-packing contacts, Adv. Appl. Bioinform. Chem. 2008, 1, 99.

110. A. Kranjc, S. Bongarzone, G. Rossetti, X. Biarnés, A. Cavalli, M. Bo- lognesi, M. Roberti, G. Legname, P. Carloni, Docking Ligands on Protein Surfaces-. The Case Study of Prion Protein, J. Chem. Theory Comput. 2009, 5, 2565.

111. L. Meireles, A. Dömling, C. Camacho, ANCHOR: a web server and database for analyis of protein-protein interaction binding pockets for drug discouvery, Nucleic Acids Res. 2010, 38, 407.