Integration of virtual and high throughput screening in lead discovery settings

Combinatorial Chemistry and High Throughput Screening

Volumn 14, Issue 10, 2011, Pages 889-897

  Polgár, Tímea ^a   Keseru, György M ^a,b  

^a BUDAPEST UNIVERSITY OF TECHNOLOGY AND ECONOMICS   (Hungary)

^b GEDEON RICHTER LTD   (Hungary)

Author keywords

Focused screening; High throughput screening; Integration; Parallel screening; Sequential screening.; Virtual screening

Indexed keywords

LIGAND;

ANALYTIC METHOD; ARTICLE; DRUG RESEARCH; HIGH THROUGHPUT SCREENING; PHARMACOPHORE; PRIORITY JOURNAL; THEORETICAL STUDY; VIRTUAL REALITY; X RAY CRYSTALLOGRAPHY;

ANIMALS; DRUG DISCOVERY; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; LIGANDS; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; PHARMACOLOGY;

EID: 80054916367     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/138620711797537148     Document Type: Article

References (54)

1. Polgár, T.; Keser , G.M. Virtual Screening, Encyclopedia of Pharmaceutical Technology, Pharmaceutical Technology, Informaworld Plc, 2006.
2. Bajorath, J. Integration of virtual and high-throughput screening. Nat. Drug Discov. Rev., 2002, 1, 882-894. (Pubitemid 37361583)
3. Polgár, T.; Keser , G.M. Structure-based virtual screening. Frontiers in Drug Design & Discovery: Structure-Based Drug Design in the 21st Century, 2007, 3(1), 477-502.
4. Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev., 1997, 23(1-3), 3-25. (Pubitemid 27046991)
5. Hann, M.M.; Leach, A. R.; Harper, G. Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery, Journal of Chemical Information and Computational Science, 2001, 41(3), 856-864.
6. Teague, S.J.; Davis, A.M.; Leeson, P.D.; Oprea, T.I. The design of leadlike combinatorial libraries. Angewandte. Chemistry, Int. Ed., 1999, 38(24), 3743-3748. (Pubitemid 30022004)
7. Walters, P.; Stahl, M.T., Murcko, M.A. Virtual screening-an overview. Drug Discov. Today, 1998, 3(4), 160-178.
8. Strategic Pooling of Compounds for High-Throughput Screening, Mike Hann, Brian Hudson, Xiao Lewell, Rob Lifely, Luke Miller, and Nigel Ramsden, Journal of Chemical Information and Computational Science, 1999, 39(5), 897-902.
9. Willett, P. Similarity-based virtual screening using 2D fingerprints. Drug Discov. Today, 2006, 11(23-24), 1046-1053. (Pubitemid 44792477)
10. Willett, P.; Barnard, J.M.; Downs, G.M. Chemical similarity searching. Journal of Chemical Information and Computer Sciences, 1998, 38(6), 983-996. (Pubitemid 128591261)
11. Cross, S. S. J. Improved FlexX docking using FlexS-determined base fragment placement. J. Chem. Inf. Model., 2005, 45(4), 993-1001. (Pubitemid 41156698)
12. Schellhammer, I.; Rarey, M. FlexX-Scan: Fast structure-based virtual screening PROTEINS: Struct. Funct. Genet., 2004, 57(3), 504-517. (Pubitemid 39390805)
13. ROCS, © 1997-2010 OpenEye Scientific Software.
14. 3D alignment, © 1999-2010 ChemAxon Ltd.
15. Lyne, P.D. Structure-based virtual screening: an overview. Drug Discov. Today, 2002, 7(20), 1047-1055.
16. Ghosh, S.; Nie, A.; An, J.; Huang, Z. Combinatorial chemistry and molecular diversity, Structure-based virtual screening of chemical libraries for drug discovery. Curr. Opin. Chem. Biol., 2006, 10(3), 194-202 (Pubitemid 43815778)
17. Olah, M.M.; Bologa, C.G.; Oprea, T.I. Strategies for compound selection. Curr. Drug Discov. Technol., 2004, 1(3), 211-220.
18. Charifson, P.S.; Walters, W.P. Filtering databases and chemical libraries. Mol. Divers., 2000, 5(4), 185-197. (Pubitemid 36076935)
19. Hann, M.; Hudson, B.; Lewell, X.; Lifely, R.; Miller, L.; Ramsden, N. Strategic Pooling of Compounds for High-Throughput Screening. J. Chem. Inf.Comput. Sci., 1999, 39(5), 897-902.
20. Andrews, P.R.; Craik, D.J.; Martin, J.L. Functional group contributions to drug-receptor interactions. J. Med. Chem., 1984, 27(12), 1648-1657. (Pubitemid 15177908)
21. Muegge, I.; Heald, S.L.; Brittelli, D. Simple selection criteria for drug-like chemical matter. J. Med. Chem., 2001, 44(12), 1841-1846. (Pubitemid 32884510)
22. Bleicher, K.H.; Böhm, H.J.; Müller, K.; Alanine, A.I. A guide to drug discovery: Hit and lead generation: beyond high-throughput screening. Nat. Rev. Drug Discov., 2003, 2, 369-378. (Pubitemid 37361707)
23. White, R.E. High-throughput screening in drug metabolism and pharmacokinetic support of drug discovery. Ann. Rev. Pharmacol. Toxicol., 2000, 40(133-157), 133-157. (Pubitemid 30340676)
24. Mayr, M.M. The future of high-throughput screening. J. Biomol. Screen., 2008, 13(6), 443-448.
25. Stahura, F.L.; Bajorath, J. Virtual screening methods that complement HTS. Comb. Chem. High Throughput Screen., 2004, 7(4), 259-269. (Pubitemid 38858880)
26. Heping, Z.; Burton, H.S. Recursive Partitioning and Applications. 2nd ed., Springer, 2010.
27. Chen, X.; Rusinko, A; Young, S.S. Recursive partitioning analysis of a large structure activity data set using three-dimensional descriptors. J. Chem. Inf. Comp. Sci., 1998, 38(6), 1054-1062. (Pubitemid 128591268)
28. Rusinko, A.; Farmen, M.W.; Lambert, C.G.; Brown, P.L.; Young, S.S. Analysis of a large structure/biological activity data set using recursive partitioning. J. Chem. Inf. Comp. Sci., 1999, 39(6), 1017-1026. (Pubitemid 129579834)
29. Tamura, S.Y.; Bacha, P.A.; Gruver, H.S.; Nutt, R.F. Data analysis of high-throughput screening results: Application of multidomain clustering to the NCI anti-HIV data set. J. Med. Chem., 2002, 45(14), 3082-3093. (Pubitemid 34721530)
30. Labute, P. Binary QSAR: a new method for the determination of quantitative structure activity relationships. Pac. Symp. Biocomput., 1999, 4, 444-455.
31. Xue, L.; Godden, J.; Gao, H.; Bajorath, J. Identification of a preferred set of molecular descriptors for compound classification based on principal component analysis. J. Chem. Inf. Comput. Sci., 1999, 39(4), 699-704. (Pubitemid 129539571)
32. Harper, G.; Bradshaw, J.; Gittins, J.C.; Green, D.V.S.; Leach, A.R. Prediction of biological activity for high-throughput screening using binary kernel discrimination. J. Chem. Inf. Comput. Sci., 2001, 41(5), 1295-1300.
33. Zernov, V.Z.; Balakin, K.V.; Ivaschenko, A.A.; Savchuk, N.P.; Pletnev, I.P. Drug discovery using support vector machines. The case studies of drug-likeness, agrochemical-likeness, and enzyme inhibition predictions. J. Chem. Inf. Comput. Sci., 2003, 43(6), 2048-2056.
34. Ivanciuc, O. Applications of support vector machines in chemistry. Rev. Comput. Chem., 2007, 23, 291-400.
35. Cheng, B.; Titterington, D.M. Neural networks: A review from a statistical perspective. Stat. Sci., 1994, 9(1), 2-30.
36. Doman, T.N.; Mcgovern, S.L.; Witherbee, B.J.; Kasten, T.P.; Kurumbail, R.; Stallings, W.C.; Connolly, D.T.; Shoichet, B.K. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J. Med. Chem., 2002, 45(11), 2213-2221. (Pubitemid 34525801)
37. Polgar, T.; Baki, A.; Szendrei, G.I.; Keseru G.M. Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3-inhibitors. J. Med. Chem., 2005, 48(25), 7946-7959. (Pubitemid 41798426)
38. Babaoglu, K.; Simeonov, A.; Irwin, J.J.; Nelson, M.E.; Feng, B.; Thomas, C.J.; Cancian, L.; Costi, M.P.; Maltby, D.A.; Jadhav, A.; Inglese, J.; Austin, C.P.; Shoichet, B.K. Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against-Lactamase. Journal of Medicinal Chemistry, 2008, 51(8), 2502-2511. (Pubitemid 351628511)
39. Ferreira, R.S.; Simeonov, A.; Jadhav, A.; Eidam, O.; Mott, B.T.; Keiser, M.J.; McKerrow, J.H.; Maloney, D.J.; Irwin, J.J.; K. Shoichet, B.K. Complementarity between a docking and a highthroughput screen in discovering new Cruzain inhibitors. J. Med. Chem., 2010, 53(13), 4891-4905.
40. Singh, J.; van Vlijmen, H.; Liao, Y.; Lee, W-C.; Cornebise, M.; Harris, M.; Shu, I.; Gill, A., Cuervo, J.H.; Abraham, W.M.; Adams, S.P. Identification of potent and novel 4-1 antagonists using in silico screening. J. Med. Chem. 2002, 45(14), 2988-2993. (Pubitemid 34721520)
41. Kiss, R.; Kiss, B.; Könczöl, Á.; Szalai, F.; Jelinek, I.; László, V.; Noszál, B.; Falus, A.; Keser, G.M. Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening. J. Med. Chem., 2008, 51(11), 4891-4905.
42. Stahura, F.L.; Xue, L.; Godden, J.W.; Bajorath, J. Methods for compound selection focused on hits and application in drug discovery. J. Mol. Graph. Model., 2002, 20(6), 439-446. (Pubitemid 34312059)
43. Jones-Hertzog, D.K.; Mukhopadhyay, P.; Keefer, C.E.; Young, S.S. Use of recursive partitioning in the sequential screening of Gprotein-coupled receptors. J. Pharmacol. Toxicol. Methods, 2008, 51(2), 3145-3153.
44. Engels, M.F.M.; Venkatarangan, P. Smart screening: Approaches to efficient HTS. Curr. Opin. Drug Discov. Devel., 2001, 4, 275-283. (Pubitemid 32499896)
45. Lewell, X.Q.; Judd, D.B.; Watson, S.P.; Hann, M.M. RECAPRetrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Infor. Comp. Sci., 1998, 38(3), 511-522. (Pubitemid 128594467)
46. Stanton, D.; Morris, T.W.; Roychoudhury, S.; Parker, C.N. Application of nearest-neighbour and cluster analyses in pharmaceutical lead discovery. J. Chem. Inform. Comp. Sci., 1999, 39(1), 21-27. (Pubitemid 129676553)
47. Chen, X.; Wilson, L.J.; Malaviya, R.; Argentieri, R.L., Yang, S.M. Virtual screening to successfully identify novel Janus kinase 3 inhibitors: A sequential focused screening approach. J. Med. Chem., 2008, 51, 7015-7019.
48. Good, A.C.; Krystek, S.R.; Mason, J.S. High-throughput and virtual screening: core lead discovery technologies move towards integration. Drug Discov. Today, 2000, 5(12), 61-69.
49. Poulain, R.F.; Horvath, D.; Bonnet, B.; Eckhoff, C.; Chapelain, B.; Bodinier, M-C.; Deprez, B. From hit to lead. Analyzing structureprofile relationships J. Med. Chem., 2001, 44(21), 3391-3401. (Pubitemid 32947905)
50. Manallack, D.T.; Pitt, W.R.; Gancia, E.; Montana, J.G.; Livingstone, D.J.; Ford, M.G.; Whitley, D.C. Selecting screening candidates for kinase and G protein-coupled receptor targets using neural networks. J. Chem. Inf. Comput. Sci., 2002, 42(5), 1256-62. (Pubitemid 35360310)
51. Schneider, G.; Nettekoven, M. Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using selforganizing maps. J. Comb. Chem., 2003, 5(3), 233-237. (Pubitemid 37140569)
52. Bradley, E.K.; Miller, J.L.; Saiah, E.; Grootenhuis, D.J. Informative library design as an efficient strategy to identify and optimize leads: Application to cyclin-dependent kinase 2 antagonists. J. Med. Chem., 2003, 46(20), 4360-4364. (Pubitemid 37153016)
53. Grüneberg, S.; Stubbs, M.T.; Klebe, G. Successful virtual screening for novel inhibitors of human carbonic anhydrase: Strategy and experimental confirmation. J. Med. Chem., 2002, 45(17), 3588-3602. (Pubitemid 34863232)
54. Spencer, R.W. Diversity analysis in high throughput screening. J. Biomol. Screen, 1997, 2(2), 69-70. 898-907 (Pubitemid 127689995)