Protein-protein interface analysis and hot spots identification for chemical Ligand design

Current Pharmaceutical Design

Volumn 20, Issue 8, 2014, Pages 1192-1200

  Chen, Jing ^a,b   Ma, Xiaomin ^a,b   Yuan, Yaxia ^a,b   Pei, Jianfeng ^b   Lai, Luhua ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

Binding site detection; Hot spots; Ligandability; Pocket V.3; Protein protein interface analysis; Small molecular binder

Indexed keywords

LIGAND; PROTEIN; PROTEIN BINDING;

ARTICLE; BINDING AFFINITY; BINDING SITE; HUMAN; LIGAND BINDING; PHARMACOPHORE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; DRUG DESIGN; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROCEDURES; PROTEIN DATABASE;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE;

EID: 84903698054     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/13816128113199990065     Document Type: Article

References (80)

1. Blundell TL, Burke DF, Chirgadze D, et al. Protein-protein interactions in receptor activation and intracellular signalling. Biol Chem 2000; 381: 955-9.
2. Kar G, Gursoy A, Keskin O. Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol 2009; 5: e1000601.
3. Khan SH, Ahmad F, Ahmad N, Flynn DC, Kumar R. Proteinprotein interactions: principles, techniques, and their potential role in new drug development. J Biomol Struct Dyn 2011; 28: 929-38.
4. Ma DC, Diao YB, Guo YZ, et al. A novel method to predict protein-protein interactions based on the information of proteinprotein interaction networks and protein sequence. Protein Pept Lett 2011; 18: 906-11.
5. Zhang C, Lai L. Towards structure-based protein drug design. Biochem Soc Trans 2011; 39: 1382-1386.
6. Leader B, Baca QJ, Golan DE. Protein therapeutics: a summary and pharmacological classification. Nat Rev Drug Discov 2008; 7: 21-39.
7. Strohl WR, Knight DM. Discovery and development of biopharmaceuticals: current issues. Curr Opin Biotechnol 2009; 20: 668-672.
8. Berg T. Modulation of protein-protein interactions with small organic molecules. Angew Chem Int Ed Engl 2003; 42: 2462-81.
9. Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007; 450: 1001-9.
10. Cochran AG. Antagonists of protein-protein interactions. Chem Biol 2000; 7: R85-94.
11. Toogood PL. Inhibition of protein-protein association by small molecules: approaches and progress. J Med Chem 2002; 45: 1543-58.
12. Pagliaro L, Felding J, Audouze K, et al. Emerging classes of protein-protein interaction inhibitors and new tools for their development. Curr Opin Chem Biol 2004; 8: 442-9.
13. Fry DC, Graves B, Vassilev LT. Development of E3-substrate (MDM2-p53)-binding inhibitors: structural aspects. Methods Enzymol 2005; 399: 622-33.
14. Fry DC. Protein-protein interactions as targets for small molecule drug discovery. Biopolymers 2006; 84: 535-52.
15. Zhang CC, Kast J. Applications of current proteomics techniques in modern drug design. Curr Comput Aided Drug Des 2010; 6: 147-64.
16. Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004; 3: 301-17.
17. Domling A. Small molecular weight protein-protein interaction antagonists: an insurmountable challenge? Curr Opin Chem Biol 2008; 12: 281-91.
18. Meireles LM, Mustata G. Discovery of modulators of proteinprotein interactions: current approaches and limitations. Curr Top Med Chem 2011; 11: 248-57.
19. Zhong S, Macias AT, MacKerell AD, Jr. Computational identification of inhibitors of protein-protein interactions. Curr Top Med Chem 2007; 7: 63-82.
20. Villoutreix BO, Bastard K, Sperandio O, et al. In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics. Curr Pharm Biotechnol 2008; 9: 103-22.
21. Bienstock RJ. Computational drug design targeting protein-protein interactions. Curr Pharm Des 2012; 18: 1240-54.
22. Jubb H, Higueruelo AP, Winter A, Blundell TL. Structural biology and drug discovery for protein-protein interactions. Trends Pharmacol Sci 2012; 33: 241-8.
23. Eyrisch S, Helms V. Transient pockets on protein surfaces involved in protein-protein interaction. J Med Chem 2007; 50: 3457-64.
24. Ozbabacan SE, Engin HB, Gursoy A, Keskin O. Transient proteinprotein interactions. Protein Eng Des Sel 2011; 24: 635-48.
25. Yuan Y, Pei J, Lai L. Binding site detection and druggability prediction of protein targets for structure-based drug desgin. Curr Pharm Des 2013; 19: 2326-2333.
26. Thangudu RR, Bryant SH, Panchenko AR, Madej T. Modulating protein-protein interactions with small molecules: the importance of binding hotspots. J Mol Biol 2012; 415: 443-53.
27. Brown SP, Hajduk PJ. Effects of conformational dynamics on predicted protein druggability. Chem Med Chem 2006; 1: 70-2.
28. Bowman AL, Nikolovska-Coleska Z, Zhong H, Wang S, Carlson HA. Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. J Am Chem Soc 2007; 129: 12809-14.
29. Fu X, Apgar JR, Keating AE. Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL. J Mol Biol 2007; 371: 1099-117.
30. Novak W, Wang H, Krilov G. Role of protein flexibility in the design of Bcl-X(L) targeting agents: insight from molecular dynamics. J Comput Aided Mol Des 2009; 23: 49-61.
31. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005; 15: 586-92.
32. Bahar I, Lezon TR, Yang LW, Eyal E. Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 2010; 39: 23-42.
33. Kim JI, Na S, Eom K. Domain decomposition-based structural condensation of large protein structures for understanding their conformational dynamics. J Comput Chem 2011; 32: 161-9.
34. Pommier Y, Cherfils J. Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery. Trends Pharmacol Sci 2005; 26: 138-45.
35. Block P, Weskamp N, Wolf A, Klebe G. Strategies to search and design stabilizers of protein-protein interactions: a feasibility study. Proteins 2007; 68: 170-186.
36. Cai Z, Greene MI, Berezov A. Modulation of biomolecular interactions with complex-binding small molecules. Methods 2008; 46: 39-46.
37. Pommier Y, Marchand C. Interfacial inhibitors: targeting macromolecular complexes. Nat Rev Drug Discov 2012; 11: 25-36.
38. Fenton AW. Allostery: an illustrated definition for the 'second secret of life'. Trends Biochem Sci 2008; 33: 420-425.
39. Del Sol A, Tsai CJ, Ma B, Nussinov R. The origin of allosteric functional modulation: multiple pre-existing pathways. Structure 2009; 17: 1042-50.
40. Kar, G., O. Keskin, et al. Allostery and population shift in drug discovery. Curr Opin Pharmacol 2010; 10: 715-22.
41. Tsai CJ, Del Sol A, Nussinov R. Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst 2009; 5: 207-16.
42. Maksay G. Allostery in pharmacology: thermodynamics, evolution and design. Prog Biophys Mol Biol 2011; 106: 463-73.
43. Smith NJ, Milligan G. Allostery at G protein-coupled receptor homo-and heteromers: uncharted pharmacological landscapes. Pharmacol Rev 2010; 62: 701-25.
44. Bu Z, Callaway DJ. Proteins move! Protein dynamics and longrange allostery in cell signaling. Adv Protein Chem Struct Biol 2011; 83: 163-221.
45. Pandini A, Fornili A, Fraternali F, Kleinjung J. Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J 2012; 26: 868-81.
46. Reynolds KA, McLaughlin RN, Ranganathan R. Hot spots for allosteric regulation on protein surfaces. Cell 2011; 147: 1564-75.
47. Metz A, Pfleger C, Kopitz H, Pfeiffer-Marek S, Baringhaus KH, Gohlke H. Hot spots and transient pockets: predicting the determinants of small-molecule binding to a protein-protein interface. J Chem Inf Model 2012; 52: 120-33.
48. Dunker AK, Oldfield CJ, Meng J, et al. The unfoldomics decade: an update on intrinsically disordered proteins. BMC Genomics 2008; 9 Suppl 2: S1.
49. Brady GP, Jr., Stouten PF. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000; 14: 383-401.
50. Fuller JC, Burgoyne NJ, Jackson RM. Predicting druggable binding sites at the protein-protein interface. Drug Discov Today 2009; 14: 155-61.
51. Huang B, Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 2006; 6: 19.
52. Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM. A method for localizing ligand binding pockets in protein structures. Proteins 2006; 62: 479-88.
53. Harris R, Olson AJ, Goodsell DS. Automated prediction of ligandbinding sites in proteins. Proteins 2008; 70: 1506-17.
54. Weisel M, Proschak E, Schneider G. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem Cent J 2007; 1: 7.
55. Cheng AC, Coleman RG, Smyth KT, et al, Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol 2007; 25: 71-5.
56. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998; 280: 1-9.
57. Moreira IS, Fernandes PA, Ramos MJ. Computational alanine scanning mutagenesis--an improved methodological approach. J Comput Chem 2007; 28: 644-54.
58. Meliciani, I., K. Klenin, et al. Probing hot spots on protein-protein interfaces with all-atom free-energy simulation. J Chem Phys 2009; 131: 034114.
59. Cho KI, Kim D, Lee D. A feature-based approach to modeling protein-protein interaction hot spots. Nucleic Acids Res 2009; 37: 2672-87.
60. Tuncbag N, Gursoy A, et al. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 2009; 25: 1513-20.
61. Tuncbag N, Keskin O, Gursoy A. HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Res 2010; 38(Web Server issue): W402-406.
62. Thorn, K.S. and A.A. Bogan, ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001; 17: 284-5.
63. Fischer TB, et al., The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces. Bioinformatics 2003; 19: 1453-4.
64. Darnell SJ, Page D, Mitchell JC. An automated decision-tree approach to predicting protein interaction hot spots. Proteins 2007; 68: 813-23.
65. Darnell SJ, LeGault L, Mitchell JC. KFC Server: interactive forecasting of protein interaction hot spots. Nucleic Acids Res 2008; 36(Web Server issue): W265-69.
66. Zhu X, Mitchell JC. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features. Proteins 2011; 79: 2671-83.
67. Lise S, Buchan D, Pontil M, Jones DT. Predictions of hot spot residues at protein-protein interfaces using support vector machines. PloS One 2011; 6: e16774.
68. Deng L, Guan JH, Dong QW, Zhou SG. SemiHS: an iterative semisupervised approach for predicting protein-protein interaction hot spots. Protein Pept Lett 2011; 18: 896-905.
69. Assi SA, Tanaka T, et al. PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Res 2010; 38: e86.
70. Segura J, Fernandez-Fuentes N. PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. Nucleic Acids Res 2011; 39(Database issue): D755-60.
71. Chen J, Lai L. Pocket v.2: further developments on receptor-based pharmacophore modeling. J Chem Inf Model 2006; 46: 2684-91.
72. Gao Y, Wang R, Lai L. Structure-based method for analyzing protein-protein interfaces. J Mol Model 2004; 10: 44-54.
73. Wang RX, Gao Y, Lai LH. LigBuilder: a multi-purpose program for structure-based drug design. J Mol Model 2000; 6: 498-516.
74. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985; 28: 849-57.
75. Halgren T. New method for fast and accurate binding-site identification and analysis. Chem Biol Drug Des 2007; 69: 146-8.
76. Wang RX, Liu L, Lai LH, Tang YQ. Score: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex. J Mol Model 1998; 4: 379-94.
77. Yershova A, Jain S, LaValle SM, Mitchell JC. Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration. Inter J Robot Res 2009; 28: 1-15.
78. Bourgeas R, et al., Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One 2010; 5: e9598.
79. Voet A, Zhang KY. Pharmacophore Modelling as a Virtual Screening Tool for the Discovery of Small Molecule Proteinprotein Interaction Inhibitors. Curr Pharm Des 2012; 18: 4586-98.
80. Kozakov D, Hall DR, Chuang GY, et al. Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci 2011; 108: 13528-33.