Druggability of protein-protein interactions

Understanding and Exploiting Protein-Protein Interactions as Drug Targets

Volumn , Issue , 2013, Pages 19-31

  Hamon, Veronique ^a   Morelli, Xavier ^b  

^a UNIVERSITÉ DE RENNES 1   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HUMAN COMPUTER INTERACTION;

PROTEIN-PROTEIN INTERACTIONS;

PROTEINS;

EID: 84957099788     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4155/EBO.13.193     Document Type: Chapter

References (30)

1. Bunnage ME. Getting pharmaceutical R & D back on target. Nat. Chem. Biol. 7(6), 335-339 (2011).
2. Morelli X, Hupp T. Searching for the holy grail; protein- protein interaction analysis and modulation. EMBO Rep. 13(10), 877-879 (2012).
3. Surade S, Blundell TL. Structural biology and drug discovery of difficult targets: the limits of ligandability. Chem. Biol. 19(1), 42-50 (2012).
4. Egner U, Hillig RC. A structural biology view of target drugability. Expert. Opin. Drug Discov. 3(4), 391-401 (2008).
5. Wanner J, Fry DC, Peng Z, Roberts J. Druggability assessment of protein- protein interfaces. Future Med. Chem. 3(16), 2021-2038 (2011).
6. Hajduk PJ, Huth JR, Tse C. Predicting protein druggability. Drug Discov. Today 10(23-24) 1675-1682 (2005).
7. Edfeldt FN, Folmer RH, Breeze AL. Fragment screening to predict druggability (ligandability) and lead discovery success. Drug Discov. Today 16(7-8), 284-287 (2011).
8. Volkamer A, Kuhn D, Grombacher T, Rippmann F, Rarey M. Combining global and local measures for structure-based druggability predictions. J. Chem. Inf. Model. 52(2), 360-372 (2012).
9. Krasowski A, Muthas D, Sarkar A, Schmitt S, Brenk R. DrugPred: a structure-based approach to predict protein druggability developed using an extensive nonredundant data set. J. Chem. Inf. Model. 51(11), 2829-2842 (2011).
10. Halgren T.A. Identifying and characterizing binding sites and assessing druggability. J. Chem. Inf. Model. 49(2), 377-389 (2009).
11. Chène P. Drugs targeting protein-protein interactions. Chem. Med. Chem. 1(4), 400-411 (2006).
12. Sugaya N, Kanai S, Furuya T. Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. Database (Oxford) 2012, bas034 (2012).
13. Bourgeas R, Basse M-J, Morelli X, Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS ONE 5(3), e959 (2010).
14. Basse MJ, Betzi S, Bourgeas R et al. 2P2IDB: a structural database dedicated to orthosteric modulation of protein-protein interactions. Nucleic Acids Res. 41(D1), D824-D827 (2013).
15. Fuller JC, Burgoyne NJ, Jackson RM. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today 14(3-4), 155-161 (2009).
16. Cheng AC, Coleman RG, Smyth KT et al. Structure- based maximal affinity model predicts small-molecule druggability. Nat. Biotechnol. 25(1), 71-75 (2007).
17. Kozakov D, Hall DR, Chuang GY et al. Structural conservation of druggable hot spots in protein-protein interfaces. Proc. Natl Acad. Sci. USA 108(33), 13528-13533 (2011).
18. Schmidtke P, Le Guilloux V, Maupetit J, Tufféry P. fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res. 38(Web Server issue), W582-W589 (2010).
19. Roche P, Morelli X. Protein- protein interaction inhibition (2P2I): mixed methodologies for the acceleration of lead discovery. In: In Silico Lead Discovery. Miteva M (Ed.). Bentham, 118-143 (2010).
20. Fauman EB, Rai BK, Huang ES. Structure-based druggability assessment - identifying suitable targets for small molecule therapeutics. Curr. Opin. Chem. Biol. 15(4), 463-468 (2011).
21. Laurie A, Jackson R. Q-SiteFinder: an energy- based method for the prediction of protein-ligand binding sites. Bioinformati s 21(9), 1908-1916 (2005).
22. Schmidtke P, Barril X. Understanding and predicting druggability. A high- throughput method for detection of drug binding sites. J. Med. Chem. 53(15), 5858-5867 (2010).
23. Nisius B, Sha F, Gohlke H. Structure-based computational analysis of protein binding sites for function and druggability prediction. J. Biotechnol. 159(3), 123-134 (2012).
24. Ulucan O, Eyrisch S, Helms V. Druggability of dynamic protein-protein interfaces. Curr. Pharm. Des. 18(30), 4599-4606 (2012).
25. Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172), 1001-1009 (2007).
26. Morrow JK, Zhang S. Computational prediction of protein hot spot residues. Curr. Pharm. Des. 18(9), 1255-1265 (2012).
27. Koes DR, Camacho CJ. PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res. 40(Web Server issue), W387-W392 (2012).
28. Morelli X, Bourgeas R, Roche P. Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr. Opin. Chem. Biol. 15(4), 475-481 (2011).
29. Zhang QC, Petrey D, Deng L et al. Structure-based prediction of protein-protein interactions on a genome- wide scale. Nature 490(7421), 556-560 (2012).
30. Kuzu G, Keskin O, Gursoy A, Nussinov R. Constructing structural networks of signaling pathways on the proteome scale. Curr. Opin. Struct. Biol. 22(3), 367-377 (2012).