Shaping a screening file for maximal lead discovery efficiency and effectiveness: Elimination of molecular redundancy

Journal of Chemical Information and Modeling

Volumn 52, Issue 11, 2012, Pages 2937-2949

  Bakken, Gregory A ^a   Bell, Andrew S ^b,c   Boehm, Markus ^a   Everett, Jeremy R ^b,d   Gonzales, Rosalia ^a   Hepworth, David ^a   Klug Mcleod, Jacquelyn L ^a   Lanfear, Jeremy ^b   Loesel, Jens ^b,e   Mathias, John ^a,b   Wood, Terence P ^b,f  

^a PFIZER INC   (United States)

^b PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF GREENWICH   (United Kingdom)

^e Peter Fisk Associates Limited   (United Kingdom)

^f TP and AAW Consultancy   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

ANALYTICAL METHOD; CHEMICAL SPACE; HIGH-THROUGHPUT SCREENING; NOVEL CONCEPT;

REDUNDANCY;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG DESIGN; DRUG DEVELOPMENT; MOLECULAR LIBRARY; PROBABILITY; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ALGORITHMS; COMPUTER SIMULATION; DRUG DESIGN; DRUG DISCOVERY; MODELS, MOLECULAR; PROBABILITY; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SMALL MOLECULE LIBRARIES;

EID: 84870040454     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300372a     Document Type: Article

References (65)

1. Scannell, J. W.; Blanckley, A.; Boldon, H.; Warrington, B. Diagnosing the decline in pharmaceutical R & D efficiency Nat. Rev. Drug Discovery 2012, 11, 191-200
2. Pammoli, F.; Magazzini, L.; Riccaboni, M. The productivity crisis in pharmaceutical R&D Nat. Rev. Drug Discovery 2011, 10, 428-438
3. Mullard, A. 2011 FDA Drug Approvals Nat. Rev. Drug Discovery 2012, 11, 91-94
4. Munos, B. Lessons from 60 years of pharmaceutical innovation Nat. Rev. Drug Discovery 2009, 8, 959-968
5. Pereira, D. A.; Williams, J. A. Review: historical perspectives in pharmacology. Origin and evolution of high throughput screening Br. J. Pharmacol. 2007, 152, 53-61 (Pubitemid 47339909)
6. High Throughput Screening: Methods and Protocols (Methods in Molecular Biology); Janzen, W. P., Ed.; Humana Press: NJ, 2002.
7. High-Throughput Screening in Drug Discovery (Methods and Principles in Medicinal Chemistry); Huser, J., Ed.; Wiley-VCH: Weinheim, 2006.
8. A Practical Guide to Assay Development and High-Throughput Screening in Drug Discovery (Critical Reviews in Combinatorial Chemistry); Chen, T., Ed.; CRC Press: Boca Raton, 2010.
9. Mayr, L. M.; Bojanic, D. Novel trends in high-throughput screening Curr. Opin. Pharmacol. 2009, 9, 580-588
10. Frye, S.; Crosby, M.; Edwards, T.; Juliano, R. US academic drug discovery Nat. Rev. Drug Discovery 2011, 10, 409-410
11. Brenk, R.; Schipani, A.; James, D.; Krasowski, A.; Gilbert, I. H.; Frearson, J.; Wyatt, P. G. Lessons learnt from assembling screening libraries for drug discovery for neglected diseases ChemMedChem 2008, 3, 435-444
12. Leach, A. R.; Hann, M. H. Molecular complexity and fragment-based drug discovery: ten years on Curr. Opin. Chem. Biol. 2011, 15, 489-496
13. Hajduk, P.; Greer, J. A decade of fragment-based drug design: strategic advances and lessons learned Nat. Rev. Drug Discovery 2007, 6, 211-219 (Pubitemid 46344625)
14. Coyne, A. G.; Scott, D. E.; Abell, C. Drugging challenging targets using fragment based approaches Curr. Opin. Chem. Biol. 2010, 14, 299-307
15. Larsson, A.; Jansson, A.; Åberg, A.; Norlund, P. Efficiency of hit generation and structural characterization in fragment-based drug discovery Curr. Opin. Chem. Biol. 2011, 15, 482-488
16. Schneider, G. Virtual screening: an endless staircase? Nat. Rev. Drug Discovery 2010, 9, 273-276
17. Hajduk, P. J.; Galloway, W. R. J. D.; Spring, D. R. A question of library design Nature 2011, 470, 42-43
18. Dorr, P.; Westby, M.; Dobbs, S.; Griffin, P.; Irvine, B.; Macartney, M.; Mori, J.; Rickett, G.; Smith-Burchnell, C.; Napier, C.; Webster, R.; Armour, D.; Price, D.; Stammen, B.; Wood, A.; Perros, M. Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity Antimicrob. Agents Chemother. 2005, 49, 4721-4732 (Pubitemid 41552605)
19. Schmid, E. F.; Smith, D. A. R&D technology investments: misguided and expensive or a better way to discover medicines? Drug Discovery Today 2006, 11, 775-784 (Pubitemid 44280023)
20. Macarron, R.; Banks, M. N.; Bojanic, D.; Burns, D. J.; Cirovic, D. A.; Garyantes, T.; Green, D. V. S.; Hertzberg, R. P.; Janzen, W. P.; Paslay, J. W.; Schoper, U.; Sittampalam, G. S. Impact of high-throughput screening in biomedical research Nat. Rev. Drug Discovery 2011, 10, 188-195
21. Hopkins, A. L.; Groom, C. R. The druggable genome Nat. Rev. Drug Discovery 2002, 1, 727-30 (Pubitemid 37361545)
22. Overington, J. P.; Al-Lazikani, B.; Hopkins, A. L. How many drug targets are there? Nat. Rev. Drug Discovery 2006, 5, 993-996 (Pubitemid 44835126)
23. Schuffenhauer, A.; Brown, N. Chemical diversity and biological activity Drug Discovery Today: Technol. 2006, 3, 387-395 (Pubitemid 46158394)
24. Jacoby, E.; Schuffenhauer, A.; Popov, M.; Azzaoui, K.; Havill, B.; Schopfer, U.; Engeloch, C.; Stanek, J.; Acklin, P.; Rigollier, P.; Stoll, F.; Koch, G.; Meier, P.; Orain, D.; Giger, R.; Hinrichs, J.; Malagu, K.; Zimmermann, J.; Roth, H.-J. Key aspects of the Novartis compound collection enhancement project for the compilation of a comprehensive chemogenomics drug discovery screening collection Curr. Top. Med. Chem. 2005, 5, 397-411 (Pubitemid 40753876)
25. Willett, P. Chemoinformatics: a history Wiley Interdisc. Rev.: Comput. Mol. Sci. 2011, 1, 46-56
26. Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood behavior: a useful concept for validation of molecular diversity descriptors J. Med. Chem. 1996, 39, 3049-3059 (Pubitemid 26260310)
27. Dobson, C. M. Chemical space and biology Nature 2004, 432, 824-828 (Pubitemid 40037137)
28. Lipinski, C.; Hopkins, A. Navigating chemical space for biology and medicine Nature 2004, 432, 855-861 (Pubitemid 40037141)
29. Stepan, A. F.; Walker, D. P.; Bauman, J.; Price, D. A.; Baillie, T. A.; Kalgutkar, A. S.; Aleo, M. D. Structural alert/reactive metabolite concept as applied in medicinal chemistry to mitigate the risk of idiosyncratic drug toxicity: a perspective based on the critical examination of trends in the top 200 drugs marketed in the United States Chem. Res. Toxicol. 2011, 24, 1345-1410
30. 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 Delivery Rev. 1997, 23, 3-25 (Pubitemid 27046991)
31. Ursa, O.; Rayan, A.; Goldblum, A.; Oprea, T. I. Understanding drug-likeness Wiley Interdisc. Rev.: Comput. Mol. Sci. 2011, 1, 760-781
32. Pearlman, R. S.; Smith, K. M. Novel software tools for chemical diversity Perspect. Drug Discovery Des. 1998, 9-11, 339-353 (Pubitemid 128491931)
33. Gillet, V. J. Diversity selection algorithms Wiley Interdisc. Rev.: Comput. Mol. Sci. 2011, 1, 580-589
34. Huggins, D.; Venkitaraman, A.; Spring, D. R. Rational methods for the selection of diverse screening compounds ACS Chem. Biol. 2011, 6, 208-217
35. Nilakantan, R.; Nunn, D. S. A fresh look at pharmaceutical screening library design Drug Discovery Today 2003, 8, 668-672 (Pubitemid 36969994)
36. Harper, G.; Pickett, S. D.; Green, D. V. S. Design of a compound screening collection for use in high throughput screening Comb. Chem. High Throughput Screening 2004, 7, 63-70 (Pubitemid 38332576)
37. Lipkin, M. J.; Stevens, A. P.; Livingstone, D. J.; Harris, C. J. How large does a compound collection need to be? Comb. Chem. High Throughput Screening 2008, 11, 482-493 (Pubitemid 351969365)
38. Muchmore, S. W.; Debe, D. A.; Metz, J. T.; Brown, S. P.; Martin, Y. C.; Hajduk, P. J. Application of belief theory to similarity data fusion for use in analog searching and lead hopping J. Chem. Inf. Model. 2008, 48, 941-948
39. Dempster, A. P. Upper and Lower Probabilities Induced by a Multivalued Mapping. Ann. Stat. 1968, 28, 325-339. See also Glenn Shafer at http://www.glennshafer.com/ for further references and information (accessed October 1st, 2012).
40. Sink, R.; Gobec, S.; Pečar, S.; Zega, A. False positives in the early stages of drug discovery Curr. Med. Chem. 2010, 17, 4231-55
41. Nadin, A.; Hattotuwagama, C.; Churcher, I. Lead-oriented synthesis: a new opportunity for synthetic chemistry Angew. Chem., Int. Ed. 2012, 51, 1114-1122
42. Jadhav, A.; Ferreira, R. S.; Klumpp, C.; Mott, B. T.; Austin, C. P.; Inglese, J.; Thomas, C. J.; Maloney, D. J.; Shoichet, B. K.; Simeonov, A. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease J. Med. Chem. 2010, 53, 37-51
43. Pearce, B. C.; Sofia, M. J.; Good, A. C.; Drexler, D. M.; Stock, D. A. An empirical process for the design of high-throughput screening deck filters J. Chem. Inf. Model. 2006, 46, 1060-1068 (Pubitemid 43999150)
44. Baell, J. B.; Holloway, G. A. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays J. Med. Chem. 2010, 53, 2719-2740
45. 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, 897-902
46. Huth, J. R.; Mendoza, R.; Olejniczak, E. T.; Johnson, R. W.; Cothron, D. A.; Liu, Y.; Lerner, C. G.; Chen, J.; Hajduk, P. J. ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens J. Am. Chem. Soc. 2005, 127, 217-224 (Pubitemid 40094385)
47. Blagg, J. structure-activity relationships for in vitro and in vivo toxicity Annu. Rep. Med. Chem. 2006, 41, 353-368
48. Lajiness, M.; Watson, I. Dissimilarity-based approaches to compound acquisition Curr. Opin. Chem. Biol. 2008, 12, 366-371
49. Loesel, J. Medicinal chemistry attractiveness (MCA): A new algorithm for selecting HTS hits. Personal communication, 2011.
50. Bickerton, G. R.; Paolini, G. V.; Besnard, J.; Muresan, S.; Hopkins, A. L. Quantifying the chemical beauty of drugs Nat. Chem. 2012, 4, 90-98
51. Milne, G. M., Jr. Pharmaceutical productivity - the imperative for new paradigms Annu. Rep. Med. Chem. 2003, 38, 383-396
52. Everett, J. R.; Loesel, J. Unpublished methodology in use in Pfizer since 2006, but related to the methods disclosed by Novartis in refs 53 and 54.
53. Crisman, T. J.; Jenkins, J. L.; Parker, C. N.; Hill, W. A.; Bender, A.; Deng, Z.; Nettles, J. H.; Davies, J. W.; Glick, M. ″Plate cherry picking″: a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection J. Biomol. Screening 2007, 12, 320-7 (Pubitemid 46514676)
54. Sukuru, S. C.; Jenkins, J. L.; Beckwith, R. E.; Scheiber, J.; Bender, A.; Mikhailov, D.; Davies, J. W.; Glick, M. Plate-based diversity selection based on empirical HTS data to enhance the number of hits and their chemical diversity J. Biomol. Screening 2009, 14, 690-9
55. Boehm, M.; Hepworth, D. Personal communication, 2011.
56. Yeap, S. K.; Walley, R. J.; Snarey, M.; Van Hoorn, W. P.; Mason, J. S. Designing compound subsets: comparison of random and rational approaches using statistical simulation J. Chem. Inf. Model. 2007, 47, 2149-2158 (Pubitemid 350275081)
57. Xi, H.; Lunney, E. A. The design, annotation, and application of a kinase-targeted library Methods Mol. Biol. 2011, 685, 279-91
58. Everett, J. R.; Gardner, M.; Pullen, F.; Smith, G. F.; Snarey, M.; Terrett, N. The application of non-combinatorial chemistry to lead discovery Drug Discovery Today 2001, 6, 779-785 (Pubitemid 32722220)
59. Kainkaryam, R. M.; Woolf, P. J. Pooling in high-throughput drug screening Curr. Opin. Drug Discovery Dev 2009, 12, 339-350
60. Pipeline Pilot, version 7.5; Accelrys: San Diego, CA, 2008.
61. Gardiner, E. J.; Holliday, J. D.; O'Dowd, C.; Willett, P. Effectiveness of 2D fingerprints for scaffold hopping. Future Med. Chem. 2011, 3, 405-414
62. Willett, P. Similarity-based virtual screening using 2D fingerprints Drug Discovery Today 2006, 11, 1046-1053 (Pubitemid 44792477)
63. MDL molfile; Accelrys: San Diego, CA, 2008.
64. Daylight Toolkit, version 4.94; Daylight Chemical Information Systems Inc.: Laguna Niguel, CA, 2008.
65. Leeson, P. D.; St-Gallay, S. A. The influence of the organizational factor on compound quality in drug discovery Nat. Rev. Drug Discovery 2011, 10, 749-765