2P2Idb v2: Update of a structural database dedicated to orthosteric modulation of protein-protein interactions

Database

Volumn 2016, Issue , 2016, Pages

  Basse, Marie Jeanne ^a   Betzi, Stéphane ^a   Morelli, Xavier ^a   Roche, Philippe ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

ALGORITHM; BIOLOGY; CHEMISTRY; COMPUTER INTERFACE; INTERNET; PROCEDURES; PROTEIN ANALYSIS; PROTEIN DATABASE; SOFTWARE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; INTERNET; LIGANDS; PROTEIN INTERACTION MAPPING; PROTEINS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84964897098     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/baw007     Document Type: Article

References (33)

1. Mullard, A. (2012) Protein-protein interaction inhibitors get into the groove. Nat. Rev. Drug Discov., 11, 173-175.
2. Morelli, X. and Hupp, T. (2012) Searching for the Holy Grail; protein-protein interaction analysis and modulation. EMBO Rep., 13, 877-879.
3. Laraia, L., McKenzie, G., Spring, D. R. et al. (2015) Overcoming chemical, biological, and computational challenges in the development of inhibitors targeting protein-protein interactions. Chem. Biol., 22, 689-703.
4. Arkin, M. R., Tang, Y. and Wells, J. A. (2014) Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem. Biol., 21, 1102-1114.
5. Zhang, X., Betzi, S., Morelli, X. et al. (2014) Focused chemical libraries-design and enrichment: an example of proteinprotein interaction chemical space. Future Med. Chem., 6, 1291-1307.
6. Kuenemann, M. A., Sperandio, O., Labbé, C. M. et al. (2015) In silico design of low molecular weight protein-protein interaction inhibitors: overall concept and recent advances. Prog. Biophys. Mol. Biol, 119, 20-32.
7. Sperandio, O., Villoutreix, B. O., Morelli, X. et al. (2015) Chemical libraries dedicated to protein-protein interactions. Med. Sci., 31, 312-319.
8. Morelli, X., Bourgeas, R. and Roche, P. (2011) Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr. Opin. Chem. Biol., 15, 475-481.
9. Wilson, C. G. and Arkin, M. R. (2013) Probing structural adaptivity at PPI interfaces with small molecules. Drug Discov. Today Technol., 10, e501-e508.
10. Ottmann, C. (2013) Small-molecule modulation of protein-protein interactions. Drug Discov. Today Technol., 10, e499-e500.
11. Zinzalla, G. (2013) Understanding and Exploiting Protein-Protein Interactions as Drug Targets. London, UK (Future Science Ltd) 2-4 eBook ISBN: 978-1-909453-46-3.
12. Buchwald, P. (2010) Small-molecule protein-protein interaction inhibitors: therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations. IUBMB Life, 62, 724-731.
13. Clackson, T. and Wells, J. A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
14. Wells, J. A. and McClendon, C. L. (2007) Reaching for highhanging fruit in drug discovery at protein-protein interfaces. Nature, 450, 1001-1009.
15. Jayatunga, M. K., Thompson, S. and Hamilton, A. D. (2014) a-Helix mimetics: outwards and upwards. Bioorg. Med. Chem. Lett., 24, 717-724.
16. Lao, B. B., Drew, K., Guarracino, D. A. et al. (2014) Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. J. Am. Chem. Soc., 136, 7877-7888.
17. Szilágyi, A., Nussinov, R. and Csermely, P. (2013) Allo-network drugs: extension of the allosteric drug concept to protein-protein interaction and signaling networks. Curr. Top. Med. Chem., 13, 64-77.
18. Nussinov, R. and Tsai, C. J. (2014) Unraveling structural mechanisms of allosteric drug action. Trends Pharmacol Sci, 35, 256-264.
19. Basse, M. J., Betzi, S., Bourgeas, R. et al. (2013) 2P2Idb: a structural database dedicated to orthosteric modulation of proteinprotein interactions. Nucleic Acids Res., 41, D824-D827.
20. Bourgeas, R., Basse, M. J., Morelli, X. et al. (2010) Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One, 5, e9598.
21. Rose, P. W., Bi, C., Bluhm, W. F. et al. (2013) The RCSB protein data bank: new resources for research and education. Nucleic Acids Res., 41, D475-D482.
22. Berman, H. M., Kleywegt, G. J., Nakamura, H. et al. (2013) The future of the protein data bank. Biopolymers, 99, 218-222.
23. Higueruelo, A. P., Jubb, H. and Blundell, T. L. (2013) TIMBAL v2: update of a database holding small molecules modulating proteinprotein interactions. Database, 2013, bat039.
24. Higueruelo, A. P., Schreyer, A., Bickerton, G. R. J. et al. (2009) Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database. Chem. Biol. Drug Design, 74, 457-467.
25. Labbé, C. M., Laconde, G., Kuenemann, M. A. et al. (2013) iPPIDB: a manually curated and interactive database of small nonpeptide inhibitors of protein-protein interactions. Drug Discov. Today, 18, 958-968.
26. Hamon, V., Bourgeas, R., Ducrot, P. et al. (2014) 2P2I HUNTER: a tool for filtering orthosteric protein-protein interaction modulators via a dedicated support vector machine. J. R. Soc. Interface, 11, 20130860.
27. Hamon, V., Brunel, J. M., Combes, S. et al. (2013) 2P2Ichem: focused chemical libraries dedicated to orthosteric modulation of protein-protein interactions. Med. Chem. Comm., 4, 797-809.
28. Webb, B. and Sali, A. (2014) Protein structure modeling with MODELLER. Methods Mol. Biol., 1137, 1-15.
29. Laskowski, R. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph, 13, 323-330. 307-328.
30. Liu, Z., Li, Y., Han, L. et al. (2015) PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics, 31, 405-412.
31. Ahmed, A., Smith, R. D., Clark, J. J. et al. (2015) Recent improvements to binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res., 43, D465-D469.
32. Hu, L., Benson, M. L., Smith, R. D. et al. (2005) Binding MOAD (mother of all databases). Proteins, 60, 333-340.
33. Hsin, J., Arkhipov, A., Yin, Y. et al. (2008) Using VMD: an introductory tutorial. Curr. Protoc. Bioinformatics, Chapter 5, Unit 5.7.