Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space

Journal of Chemical Information and Modeling

Volumn 52, Issue 5, 2012, Pages 1086-1102

  Rabal, Obdulia ^a   Oyarzabal, Julen ^a  

^a UNIVERSITY OF NAVARRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

LIGANDS;

CHEMICAL BIOLOGY; LIGAND-RECEPTOR INTERACTIONS; MEDICINAL CHEMISTRY; NAVIGATION STRATEGIES; OVERLAPPING REGIONS; RELEVANT TARGET; STRUCTURAL INFORMATION; TOPOLOGICAL INFORMATION;

CHEMICAL ANALYSIS;

CELL SURFACE RECEPTOR; DRUG; LIGAND;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; HUMAN; MOLECULAR LIBRARY;

BINDING SITES; DRUG DESIGN; HUMANS; LIGANDS; MOLECULAR STRUCTURE; PHARMACEUTICAL PREPARATIONS; RECEPTORS, CELL SURFACE; SMALL MOLECULE LIBRARIES;

EID: 84861507738     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200627v     Document Type: Article

References (57)

1. Dobson, C. M. Chemical space and biology Nature 2004, 432 (7019) 824-828 (Pubitemid 40037137)
2. Kirkpatrick, P.; Ellis, C. Chemical space Nature 2004, 432 (7019) 823
3. Hert, J.; Irwin, J. J.; Laggner, C.; Keiser, M. J.; Shoichet, B. K. Quantifying biogenic bias in screening libraries Nat. Chem. Biol. 2009, 5, 479-483
4. Wetzel, S.; Bon, R. S.; Kumar, K.; Waldmann, H. Biology-oriented synthesis Angew. Chem., Int. Ed. 2011, 50, 10800-10826
5. Gorse, A. D. Diversity in medicinal chemistry space Curr. Top. Med. Chem. 2006, 6 (1) 3-18
6. Shanmugasundaram, V.; Maggiora, G. M.; Lajiness, M. S. Hit-directed nearest-neighbor searching J. Med. Chem. 2005, 48 (1) 240-248 (Pubitemid 40105262)
7. Geppert, H.; Vogt, M.; Bajorath, J. Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation J. Chem. Inf. Model. 2010, 50 (2) 205-216
8. Heikamp, K.; Bajorath, J. How do 2D fingerprints detects structurally diverse active compounds? Revealing compound subset-specific fingerprint features through systematic selection J. Chem. Inf. Model. 2011, 51 (9) 2254-2265
9. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45 (19) 4350-4358 (Pubitemid 35025581)
10. Wess, G. How to escape the bottleneck of medicinal chemistry Drug Discovery Today 2002, 7 (10) 533-535 (Pubitemid 34603638)
11. Oyarzabal, J.; Zarich, N.; Albarran, M. I.; Palacios, I.; Urbano-Cuadrado, M.; Mateos, G.; Reymundo, I.; Rabal, O.; Salgado, A.; Corrionero, A.; Fominaya, J.; Pastor, J.; Bischoff, J. R. Discovery of mitogen-activated protein kinase-interacting kinase 1 inhibitors by a comprehensive fragment-oriented virtual screening approach J. Med. Chem. 2010, 53 (18) 6618-6628
12. Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C.; Glick, M.; Davies, J. W. How similar are similarity searching methods? A principal component analysis of molecular descriptor space J. Chem. Inf. Model. 2009, 49 (1) 108-119
13. Oprea, T. I.; Gottfries, J. Chemography: The art of navigating in chemical Space J. Comb. Chem. 2001, 3 (2) 157-166 (Pubitemid 33614499)
14. Singh, N.; Guha, R.; Giulianotti, M. A.; Pinilla, C.; Houghten, R. A.; Medina-Franco, J. L. Chemoinformatic analysis of combinatorial libraries, drugs, natural products, and molecular libraries small molecule repository J. Chem. Inf. Model. 2009, 49 (4) 1010-1024
15. Le Guilloux, V.; Colliandre, L.; Bourg, S.; Guénegou, G.; Dubois-Chevalier, J.; Morin-Allory, L. Visual characterization and diversity quantification of chemical libraries: 1. Creation of delimited reference chemical subspaces J. Chem. Inf. Model. 2011, 51 (8) 1762-1774
16. Medina-Franco, J. L.; Martínez-Mayorga, K.; Giulianotti, M. A.; Houghten, R. A.; Pinilla, C. Visualization of the chemical space in drug discovery Curr. Comput.-Aided Drug Des. 2008, 4 (4) 322-333
17. Akella, L. B.; DeCaprio, D. Cheminformatics approaches to analyze diversity in compound screening libraries Curr. Opin. Chem. Biol. 2010, 14 (3) 325-330
18. Van der Horst, E.; Okuno, Y.; Bender, A.; Ijzerman, A. P. Substructure mining of GPCR ligands reveals activity-class specific functional groups in an unbiased manner J. Chem. Inf. Model. 2009, 49 (2) 348-360
19. Lameijer, E. W.; Kok, J. N.; Bäck, T.; Ijzerman, A. P. Mining a chemical database for fragment co-occurrence: Discovery of "chemical clichés" J. Chem. Inf. Model. 2006, 46 (2) 553-562
20. Lipkus, A. H.; Yuan, Q.; Lucas, K. A.; Funk, S. A.; Bartelt, W. F.; Schenck, R. J.; Trippe, A. J. Structural diversity of organic chemistry. A scaffold analysis of the CAS Registry J. Org. Chem. 2008, 73 (12) 4443-4451 (Pubitemid 351842458)
21. Xu, Y. J.; Johnson, M. Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries J. Chem. Inf. Comput. Sci. 2002, 42 (4) 912-926 (Pubitemid 35355241)
22. Roberts, G.; Myatt, G. J.; Johnson, W. P.; Cross, K. P.; Blower, P. E., Jr. LeadScope: Software for exploring large sets of screening data J. Chem. Inf. Comput. Sci. 2000, 40 (6) 1302-1314
23. Pastor, J.; Oyarzabal, J.; Martinez, S. Navigating MedChem Space: Key for Multi-Factorial Optimization in Drug Discovery. Presented at the Computer-Aided Drug Design Gordon Research Conference [Online], Tilton, NH, July 31-August 5, 2005. http://www.grc.org/programs.aspx?year=2005&program=cadd (accessed December 22, 2011).
24. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242 (Pubitemid 30047768)
25. Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: A simplified potential approach J. Med. Chem. 1999, 42 (5) 791-804 (Pubitemid 29136170)
26. Muegge, I. PMF scoring revisited J. Med. Chem. 2006, 49 (20) 5895-5902 (Pubitemid 44484936)
27. Yang, C. Y.; Wang, R.; Wang, S. M-Score: A knowledge-based potential scoring function accounting for protein atom mobility J. Med. Chem. 2006, 49 (20) 5903-5911 (Pubitemid 44484937)
28. Ghose, A. K.; Viswanadhan, V. N.; Wendoloski, J. J. A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases J. Comb. Chem. 1999, 1 (1) 55-68
29. Weininger, D. SMILES 1. Introduction and encoding rules J. Chem. Inf. Comput. Sci. 1988, 28 (1) 31-36
30. Weininger, D.; Weininger, A.; Weininger, J. L. SMILES. 2. Algorithm for generation of unique SMILES notation J. Chem. Inf. Comput. Sci. 1989, 29 (2) 97-101
31. Zuccotto, F.; Ardini, E.; Casale, E.; Angiolini, M. Through the "gatekeeper door": Exploiting the active kinase conformation J. Med. Chem. 2010, 53 (7) 2681-2694
32. Oyarzabal, J.; Howe, T.; Alcazar, J.; Andrés, J. I.; Alvarez, R. M.; Dautzenberg, F.; Iturrino, L.; Martínez, S.; Van der Linden, I. Novel approach for chemotype hopping based on annotated databases of chemically feasible fragments and a prospective case study: New melanin concentrating hormone antagonists J. Med. Chem. 2009, 52 (7) 2076-2089
33. Kibbey, C.; Calvet, A. Molecular property eXplorer: A novel approach to visualizing SAR using tree-maps and heatmaps J. Chem. Inf. Model. 2005, 45 (2) 523-532 (Pubitemid 40635360)
34. MACCS-II Database System, version 1; Molecular Design Limited: San Leandro, CA, 1984.
35. Pipeline Pilot, version 8.5; Accelrys: San Diego, CA, 2011.
36. Neudert, G.; Klebe, G. DSX: A knowledge-based scoring function for the assessment of protein-ligand complexes J. Chem. Inf. Model. 2011, 51 (10) 2731-2745
37. Wang, L.; Xie, Z.; Wipf, P.; Xie, X. Q. Residue preference mapping of ligand fragments in the Protein Data Bank J. Chem. Inf. Model. 2011, 51 (4) 807-815
38. Fan, H.; Schneidman-Duhovny, D.; Irwin, J. J.; Dong, G.; Shoichet, B. K.; Sali, A. Statistical potential for modeling and ranking of protein-ligand interactions J. Chem. Inf. Model. 2011, 51 (12) 3078-3092
39. Yamanishi, Y.; Pauwels, E.; Saigo, H.; Stoven, V. Extracting sets of chemical substructures and protein domains governing drug-target interactions J. Chem. Inf. Model. 2011, 51 (5) 1183-1194
40. Neudert, G.; Klebe, G. Fconv: Format conversion, manipulation and feature computation of molecular data Bioinformatics 2011, 27, 1021-1022
41. ChEMBL; European Bioinformatics Institute (EBI): Cambridge, 2010. http://www.ebi.ac.uk/chembl (accessed December 22, 2011).
42. Okuno, Y.; Tamon, A.; Yabuuchi, H.; Niijima, S.; Minowa, Y.; Tonomura, K.; Kunimoto, R.; Feng, C. GLIDA: GPCR ligand database for chemical genomics drug discovery database and tools update Nucleic Acids Res. 2008, 36 (suppl-1) D907-912
43. Kinase Knowledgebase (KKB); Eidogen-Sertanty, Inc: San Diego, CA, 2011.
44. Wheeler, D. L.; Barrett, T.; Benson, D. A.; Bryant, S. H.; Canese, K.; Chetvernin, V.; Church, D. M.; DiCuccio, M.; Edgar, R.; Federhen, S.; Feolo, M.; Geer, L. Y.; Helmberg, W.; Kapustin, Y.; Khovayko, O.; Landsman, D.; Lipman, D. J.; Madden, T. L.; Maglott, D. R.; Miller, V.; Ostell, J.; Pruitt, K. D.; Schuler, G. D.; Shumway, M.; Sequeira, E.; Sherry, S. T.; Sirotkin, K.; Souvorov, A.; Starchenko, G.; Tatusov, R. L.; Tatusova, T. A.; Wagner, L.; Yaschenko, E. Database resources of the National Center for Biotechnology Information Nucleic Acids Res. 2008, 36 (Database issue) D13-D21
45. Roth, B. L.; Lopez, E.; Beischel, S.; Westkaemper, R. B.; Evans, J. M. Screening the receptorome to discover the molecular targets for plant-derived psychoactive compounds: a novel approach for CNS drug discovery Pharmacol. Ther. 2004, 102 (2) 99-110 (Pubitemid 38681010)
46. Agrafiotis, D. K.; Shemanarev, M.; Connolly, P. J.; Farnum, M.; Lobanov, V. S. SAR maps: A new SAR visualization technique for medicinal chemists J. Med. Chem. 2007, 50 (24) 5926-5937
47. Schuffenhauer, A.; Ertl, P.; Roggo, S.; Wetzel, S.; Koch, M. A.; Waldmann, H. The scaffold tree-visualization of the scaffold universe by hierarchical scaffold classification J. Chem. Inf. Model. 2007, 47 (1) 47-58 (Pubitemid 46225559)
48. Clark, A. M.; Labute, P. Detection and assignment of common scaffolds in project databases of lead molecules J. Med. Chem. 2009, 52 (2) 469-483
49. Barker, E. J.; Buttar, D.; Cosgrove, D. A.; Gardiner, E. J.; Kitts, P.; Willett, P.; Gillet, V. J. Scaffold hopping using clique detection applied to reduced graphs J. Chem. Inf. Model. 2006, 46 (2) 503-511
50. Bemis, G. W.; Murcko, M. A. The properties of known drugs. 1. Molecular frameworks J. Med. Chem. 1996, 39 (15) 2887-2893 (Pubitemid 26251026)
51. Aronov, A. M.; McClain, B.; Moody, C. S.; Murcko, M. A. Kinase-likeness and kinase-privileged fragments: Toward virtual polypharmacology J. Med. Chem. 2008, 51 (5) 1214-1222 (Pubitemid 351480383)
52. Vieth, M.; Erickson, J.; Wang, J.; Webster, Y.; Mader, M.; Higgs, R.; Watson, I. Kinase inhibitor data modeling and de Novo inhibitor design with fragment approaches J. Med. Chem. 2009, 52 (20) 6456-6466
53. Schnur, D. M.; Hermsmeier, M. A.; Tebben, A. J. Are target-family- privileged substructures truly privileged? J. Med. Chem. 2006, 49 (6) 2000-2009
54. Sutherland, J. J.; Higgs, R. E.; Watson, I.; Vieth, M. Chemical fragments as foundations for understanding target space and activity prediction J. Med. Chem. 2008, 51 (9) 2689-2700 (Pubitemid 351620791)
55. Sheridan, R. P. Finding multiactivity substructures by mining databases of drug-like compounds J. Chem. Inf. Comput. Sci. 2003, 43 (3) 1037-1050
56. Yun, C. H.; Boggon, T. J.; Li, Y.; Woo, M. S.; Greulich, H.; Meyerson, M.; Eck, M. J. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity Cancer Cell 2007, 11 (3) 217-227 (Pubitemid 46349842)
57. Klabunde, T.; Hessler, G. Drug design strategies for targeting G-protein-coupled receptors ChemBioChem 2002, 3 (10) 928-944 (Pubitemid 35189597)