475
Views
12
CrossRef citations to date
0
Altmetric
Technology Evaluations

Streamlining hit discovery and optimization with a yoctoliter scale DNA reactor

, PhD & , PhD
Pages 1201-1213 | Published online: 13 Sep 2009

Bibliography

  • Kirchmair J, Distinto S, Schuster D, Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates. Curr Med Chem 2008;15(20):2040-53
  • Hajduk P, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 2007;6(3):211-9
  • Hajduk P, Greer J. Fragment-based approach to drug lead discovery: overview and advances in various techniques. Drugs R D 2008;9(4):217-27
  • Hartshorn MJ, Murray CW, Cleasby A, Fragment-based lead discovery using X-ray crystallography. J Med Chem 2005;48(2):403-13
  • Pellecchia M. Fragment-based drug discovery takes a virtual turn. Nat Chem Biol 2009;5(5):274-5
  • Zoete V, Grosdidier A, Michielin O. Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med 2009;13(2):238-48
  • Bleicher KH, Bohm HJ, Muller K, Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2003;2(5):369-78
  • Keseru G, Makara G. The influence of lead discovery strategies on the properties of drug candidates. Nat Rev 2009;8:203-12
  • Melkko S, Dumelin CE, Scheuermann J, Lead discovery by DNA-encoded chemical libraries. Drug Discov Today 2007;12(11-12):465-71
  • Houston JG, Banks MN, Binnie A, Case study: impact of technology investment on lead discovery at Bristol-Myers Squibb, 1998-2006. Drug Discov Today 2008;13(1-2):44-51
  • Sewing A, Winchester T, Carnell P, Helping science to succeed: improving processes in R&D. Drug Discov Today 2008;13(5-6):227-33
  • Macarron R. Critical review of the role of HTS in drug discovery. Drug Discov Today 2006;11(7-8):277-9
  • Eichman BF, Vargason JM, Mooers BH, The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions. Proc Natl Acad Sci USA 2000;97(8):3971-6
  • Ho PS, Eichman BF. The crystal structures of DNA Holliday junctions. Curr Opin Struct Biol 2001;11(3):302-8
  • Lipinski CA, Lombardo F, Dominy BW, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001;46(1-3):3-26
  • Veber DF, Johnson SR, Cheng HY, Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 2002;45(12):2615-23
  • Hansen MH, Blakskjaer P, Petersen LK, A Yoctoliter-Scale DNA Reactor for Small-Molecule Evolution. JACS 2009;131(3):1322-7
  • Geldenhuys WJ, Gaasch KE, Watson M, Optimizing the use of open-source software applications in drug discovery. Drug Discov Today 2006;11(3-4):127-32
  • Ghose AK, Herbertz T, Salvino JM, Knowledge-based chemoinformatic approaches to drug discovery. Drug Discov Today 2006;11(23-24):1107-14
  • Hohman M, Gregory K, Chibale K, Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Drug Discov Today 2009;14(5-6):261-70
  • Wrenn SJ, Weisinger RM, Halpin DR, Synthetic ligands discovered by in vitro selection. J Am Chem Soc 2007;129(43):13137-43
  • Mannocci L, Zhang Y, Scheuermann J, High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc Nat Acad Sci 2008;105(46):17670-5
  • Clark M, inventor Praecis Pharmaceuticals, assignee. Aurora kinase inhibitors from an encoded small molecule library. 2008 07-02-2008
  • Halpin DR, Harbury PB. DNA display I. Sequence-encoded routing of DNA populations. PLoS Biol 2004;2(7):E173
  • Gartner ZJ, Liu DR. The generality of DNA-templated synthesis as a basis for evolving non-natural small molecules. J Am Chem Soc 2001;123(28):6961-3
  • Li X, Liu DR. DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. Angew Chem Int Ed Engl 2004;43(37):4848-70
  • Snyder TM, Tse BN, Liu DR. Effects of template sequence and secondary structure on DNA-templated reactivity. J Am Chem Soc 2008;130(4):1392-401
  • Snowden M, Green D. The impact of diversity-based, high-throughput screening on drug discovery: “chance favours the prepared mind”. Curr Opin Drug Discov Dev 2008;11(4):553-8
  • Davies K. In praise of chemical diversity. 2004. Available from: www.bio-itworld.com/archive/ 081804/firstbase.html/ [cited]
  • Irwin J. How good is your screening library? Curr Opin Chem Biol 2006;10:352-6
  • Sheets M. Efficient construction of a large nonimmune phage antibody library: the production of high-affinity human single-chain antibodies to protein antigens. Proc Nat Acad Sci 1998;95:6157-62
  • Vaughan T. Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library. Nat Biotechnol 1996;14:309-14
  • Lipkin M, Stevens A, Livingstone D, How large does a compound screening collection need to be? Comb Chem High Throughput Screen 2008;11:482-93
  • Pavlou AK, Belsey MJ. The therapeutic antibodies market to 2008. Eur J Pharm Biopharm 2005;59(3):389-96
  • Maggon K. Monoclonal antibody “gold rush”. Curr Med Chem 2007;14(18):1978-87
  • Gartner ZJ, Tse BN, Grubina R, DNA-templated organic synthesis and selection of a library of macrocycles. Science 2004;305(5690):1601-5
  • Halpin DR, Harbury PB. DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution. PLoS Biol 2004;2(7):E174
  • Halpin DR, Lee JA, Wrenn SJ, DNA display III. Solid-phase organic synthesis on unprotected DNA. PLoS Biol 2004;2(7):E175
  • Tse BN, Snyder TM, Shen Y, Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection. J Am Chem Soc 2008;130(46):15611-26
  • Johnson M, Lajiness M, Maggiora G. Molecular similarity: a basis for designing drug screening programs. Prog Clin Biol Res 1989;291:167-71
  • Engels MF, Thielemans T, Verbinnen D, CerBeruS: a system supporting the sequential screening process. J Chem Inf Comput Sci 2000;40(2):241-5
  • Makara GM, Athanasopoulos J. Improving success rates for lead generation using affinity binding technologies. Curr Opin Biotechnol 2005;16(6):666-73
  • Comess K, Schurdak M. Affinity-based screening techniques for enhancing lead discovery. Curr Opin Drug Discov Dev 2004;7(4):411-6
  • Heitner T, Moor A, Garrison JL, Selection of cell binding and internalizing epidermal growth factor receptor antibodies from a phage display library. J Immunol Meth 2001;248(1-2):17-30
  • Heitner T, Satozawa N, McLean K, Obligate multivalent recognition of cell surface tomoregulin following selection from a multivalent phage antibody library. J Biomol Screen 2006;11(8):985-95
  • Schwarz M, Rottgen P, Takada Y, Single-chain antibodies for the conformation-specific blockade of activated platelet integrin alphaIIbbeta3 designed by subtractive selection from naive human phage libraries. FASEB J 2004;18(14):1704-6
  • Marks JD. Selection of internalizing antibodies for drug delivery. Methods Mol Biol 2004;248:201-8
  • Poul MA, Becerril B, Nielsen UB, Selection of tumor-specific internalizing human antibodies from phage libraries. J Mol Biol 2000;301(5):1149-61
  • Bender A, Bojanic D, Davies JW, Which aspects of HTS are empirically correlated with downstream success? Curr Opin Drug Discov Dev 2008;11(3):327-37
  • Fox S, Farr-Jones S, Sopchak L, High-throughput screening: update on practices and success. J Biomol Screen 2006;11(7):864-9
  • Harvey AL. Natural products in drug discovery. Drug Discov Today 2008;13(19-20):894-901
  • van Montfort RL, Workman P. Structure-based design of molecular cancer therapeutics. Trends Biotechnol 2009;27(5):315-28

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.