Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 245-

  Quintus, Flavien ^a   Sperandio, Olivier ^a   Grynberg, Julien ^a   Petitjean, Michel ^b   Tuffery, Pierre ^a  

^a INSERM   (France)

^b CEA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE COMPOUNDS; CHEMICAL LIBRARIES; MOLECULAR SIMILARITY; PHYSICO-CHEMICALS; SCIENTIFIC COMMUNITY; SEARCH ALGORITHMS; SIMILARITY SEARCH; VIRTUAL SCREENING;

LIGANDS; RESEARCH; TOOLS;

THREE DIMENSIONAL;

LIGAND; MOLECULAR SCAFFOLD;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; CONFORMATION; INTERNET; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; PHYSICAL CHEMISTRY; SCREENING; SEARCH ENGINE; SENSITIVITY ANALYSIS;

COMPUTATIONAL BIOLOGY; DRUG DESIGN; DRUG DISCOVERY; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; SMALL MOLECULE LIBRARIES;

EID: 70349745554     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-245     Document Type: Article

References (30)

1. Rester U. From virtuality to reality - Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr Opin Drug Discov Devel 2008, 11(4):559-68.
2. Sittampalam G.S, Kahl S.D, Janzen W.P. High-throughput screening: advances in assay technologies. Curr Opin Chem Biol 1997, 1(3):384-91. 10.1016/S1367-5931(97)80078-6, 9667878.
3. Blundell T.L, Jhoti H, Abell C. High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Discov 2002, 1:45-54. 10.1038/nrd706, 12119609.
4. Nefzi A, Dooley C, Ostresh J.M, Houghten R.A. Combinatorial chemistry: from peptides and peptidomimetics to small organic and heterocyclic compounds. Bioorg Med Chem Lett 1998, 8(17):2273-8. 10.1016/S0960-894X(98)00412-0, 9873527.
5. Sperandio O, Miteva M.A, Delfaud F, Villoutreix B.O. Receptor-based computational screening of compound databases: the main docking-scoring engines. Curr Protein Pept Sci 2006, 7(5):369-93. 10.2174/138920306778559377, 17073691.
6. Stockwell B.R. Chemical genetics: ligand-based discovery of gene function. Nat Rev Genet 2000, 1(2):116-25. 10.1038/35038557, 11253651.
7. Esposito E.X, Hopfinger A.J, Madura J.D. Methods for applying the quantitative structure-activity relationship paradigm. Methods Mol Biol 2004, 275:131-214. full_text, 15141113.
8. Girke T, Cheng L.C, Raikhel N. ChemMine. A compound mining database for chemical genomics. Plant Physiol 2005, 138(2):573-7. 10.1104/pp.105.062687, 1150377, 15955920.
9. Lemmen C, Lengauer T, Klebe G. FLEXS: a method for fast flexible ligand superposition. J Med Chem 1998, 41(23):4502-20. 10.1021/jm981037l, 9804690.
10. Sperandio O, Andrieu O, Miteva M.A, Vo M.Q, Souaille M, Delfaud F, Villoutreix B.O. MED-SuMoLig: a new ligand-based screening tool for efficient scaffolds hopping. J Chem Inf Model 2007, 47(3):1097-110. 10.1021/ci700031v, 17477521.
11. ROCS version 2.2. 2006,
12. Cheeseright T.J, Mackey M.D, Melville J.L, Vinter J.G. FieldScreen: virtual screening using molecular fields. Application to the DUD data set. J Chem Inf Model 2008, 48(11):2108-17. 10.1021/ci800110p, 18991371.
13. Khedkar S.A, Malde A.K, Coutinho E.C, Srivastava S. Pharmacophore modeling in drug discovery and development: an overview. Med Chem 2007, 3(2):187-97. 10.2174/157340607780059521, 17348856.
14. Jain A.N. Ligand-based structural hypotheses for virtual screening. J Med Chem 2004, 47(4):947-61. 10.1021/jm030520f, 14761196.
15. Petitjean M. Interactive Maximal Common 3D Substructure Searching with the Combined SDM/RMS Algorithm. Comp Chem 1998, 22:463-465.
16. Escalier V, Pothier J, Soldano H, Viari A. Pairwise and multiple identification of three-dimensional common substructures in proteins. J Comput Biol 1998, 5:41-56. 10.1089/cmb.1998.5.41, 9541870.
17. Sheridan R.P, McGaughey G.B, Cornell W.D. Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results. J Comput Aided Mol Des 2008, 22(3-4):257-65. 10.1007/s10822-008-9168-9, 18273559.
18. Willett P. Searching techniques for databases of two- and three-dimensional chemical structures. J Med Chem 2005, 48(13):4183-99. 10.1021/jm0582165, 15974568.
19. Knegtel R.M, Wagener M. Efficacy and selectivity in flexible database docking. Proteins 1999, 37(3):334-45. 10.1002/(SICI)1097-0134(19991115)37:3<334::AID-PROT3>3.0.CO;2-9, 10591095.
20. Knox A.J, Meegan M.J, Carta G, Lloyd D.G. Considerations in compound database preparation-"hidden" impact on virtual screening Results. J Chem Inf Model 2005, 45(6):1908-19. 10.1021/ci050185z, 16309298.
21. McGaughey G.B, Sheridan R.P, Bayly C.I, Culberson J.C, Kreatsoulas C, Lindsley S, Maiorov V, Truchon J.F, Cornell W.D. Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 2007, 47(4):1504-19. 10.1021/ci700052x, 17591764.
22. Maignan S, Guilloteau J.P, Choi-Sledeski Y.M, Becker M.R, Ewing W.R, Pauls H.W, Spada A.P, Mikol V. Molecular structures of human factor Xa complexed with ketopiperazine inhibitors: preference for a neutral group in the S1 pocket. J Med Chem 2003, 46(5):685-90. 10.1021/jm0203837, 12593649.
23. Reich S.H, Melnick M, Davies J.F, Appelt K, Lewis K.K, Fuhry M.A, Pino M, Trippe A.J, Nguyen D, Dawson H. Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease. Proc Natl Acad Sci USA 1995, 92(8):3298-302. 10.1073/pnas.92.8.3298, 42153, 7724556.
24. Stoll V, Stewart K.D, Maring C.J, Muchmore S, Giranda V, Gui Y, Gu Y, Wang G, Chen Y, Sun M, Zhao C, Kennedy A.L, Madigan D.L, Xu Y, Saldivar A, Kati W, Laver G, Sowin T, Sham H.L, Greer J, Kempf D. Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series. Biochemistry 2003, 42(3):718-27. 10.1021/bi0205449, 12534284.
25. Stubbs M.T, Reyda S, Dullweber F, Möller M, Klebe G, Dorsch D, Mederski W.W, Wurziger H. pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design. Chembiochem 2002, 3(2-3):246-9. 10.1002/1439-7633(20020301)3:2/3<246::AID-CBIC246>3.0.CO;2-#, 11921406.
26. Miteva M.A, Violas S, Montes M, Gomez D, Tuffery P, Villoutreix B.O. FAF-Drugs: free ADME/tox filtering of compound collections. Nucleic Acids Res 2006, 34:W738-44. 10.1093/nar/gkl065, 1538885, 16845110.
27. Verdonk M.L, Hartshorn M.J. Structure-guided fragment screening for lead discovery. Curr Opin Drug Discov Devel 2004, 7(4):404-10.
28. Miller M.D, Sheridan R.P, Kearsley S.K. SQ: a program for rapidly producing pharmacophorically relevent molecular superpositions. J Med Chem 1999, 42(9):1505-14. 10.1021/jm9806143, 10229621.
29. Rhodes N, Willett P, Calvet A, Dunbar J.B, Humblet C. CLIP: similarity searching of 3D databases using clique detection. J Chem Inf Comput Sci 2003, 43(2):443-8.
30. Guha R, Howard M.T, Hutchison G.R, Murray-Rust P, Rzepa H, Steinbeck C, Wegner J, Willighagen E.L. The Blue Obelisk-interoperability in chemical informatics. J Chem Inf Model 2006, 46(3):991-8. 10.1021/ci050400b, 16711717.