Design, synthesis and selection of DNA-encoded small-molecule libraries (original) (raw)

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In the version of this article initially published, the IC50 values in the table in Figure 3c were listed as nM instead of μM. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Smith, G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 (1985).
    Article CAS Google Scholar
  2. Barbas, C.F. III. Recent advances in phage display. Curr. Opin. Biotechnol. 4, 526–530 (1993).
    Article CAS Google Scholar
  3. Wilson, D.S., Keefe, A.D. & Szostak, J.W. The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl. Acad. Sci. USA 98, 3750–3755 (2001).
    Article CAS Google Scholar
  4. Frankel, A., Li, S., Starck, S.R. & Roberts, R.W. Unnatural RNA display libraries. Curr. Opin. Struct. Biol. 13, 506–512 (2003).
    Article CAS Google Scholar
  5. Ellington, A.D. & Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990).
    Article CAS Google Scholar
  6. Joyce, G.F. Amplification, mutation and selection of catalytic RNA. Gene 82, 83–87 (1989).
    Article CAS Google Scholar
  7. Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510 (1990).
    Article CAS Google Scholar
  8. Brenner, S. & Lerner, R.A. Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89, 5381–5383 (1992).
    Article CAS Google Scholar
  9. Melkko, S., Dumelin, C.E., Scheuermann, J. & Neri, D. Lead discovery by DNA-encoded chemical libraries. Drug Discov. Today 12, 465–471 (2007).
    Article CAS Google Scholar
  10. Li, X. & Liu, D.R. DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules. Angew. Chem. Int. Ed. 43, 4848–4870 (2004).
    Article CAS Google Scholar
  11. Halpin, D.R., Lee, J.A., Wrenn, S.J. & Harbury, P.B. DNA display. III. Solid-phase organic synthesis on unprotected DNA. PLoS Biol. 2, 1031–1038 (2004).
    CAS Google Scholar
  12. Wrenn, S.J., Weisinger, R.W., Halpin, D.R. & Harbury, P.B. Synthetic ligands discovered by in vitro selection. J. Am. Chem. Soc. 129, 13137–13143 (2007).
    Article CAS Google Scholar
  13. Melkko, S., Scheurmann, J., Dumelin, C.E. & Neri, D. Encoded self-assembling chemical libraries. Nat. Biotechnol. 22, 568–574 (2004).
    Article CAS Google Scholar
  14. Buller, F. et al. Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions. Bioorg. Med. Chem. Lett. 18, 5926–5931 (2008).
    Article CAS Google Scholar
  15. Hansen, M.H. et al. A Yoctoliter-scale DNA reactor for small-molecule evolution. J. Am. Chem. Soc. 131, 1322–1327 (2009).
    Article CAS Google Scholar
  16. Morgan, B. et al. Synthesis of combinatorial libraries containing encoding oligonucleotide tags. WO patent application 2007/053358 (2007).
  17. Kinoshita, Y. & Nishigaki, K. Enzymic synthesis of code regions for encoded combinational chemistry (ECC). in Nucleic Acids Symposium Series No. 34, 201–202 (Oxford University Press, Oxford, 1995).
  18. Leftheris, K. et al. The discovery of orally active triaminotriazine aniline amides as inhibitors of p38 MAP kinase. J. Med. Chem. 47, 6283–6291 (2004).
    Article CAS Google Scholar
  19. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
    Article CAS Google Scholar
  20. Mannoci, L. et al. High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc. Natl. Acad. Sci. USA 105, 17670–17675 (2008).
    Article Google Scholar
  21. Harrington, E. et al. VX-680, a potent and selective small-molecule inhibitor of the Aurora kinases, suppresses tumor growth in vivo. Nat. Med. 10, 262–267 (2004).
    Article CAS Google Scholar
  22. Mortlock, A.A. et al. Progress in the development of selective inhibitors of Aurora Kinases. Curr. Top. Med. Chem. 5, 807–821 (2005).
    Article CAS Google Scholar
  23. Burns, C.J., Wilks, A.F. & Bu, X. Preparation of pyrazine derivatives as kinase inhibitors. WO patent 2005/054230 (2005).
  24. Western, E.C., Daft, J.R., Johnson, E.M., II, Gannett, P.M. & Shaughnessy, K.H. Efficient one-step Suzuki arylation of unprotected halonucleosides, using water-soluble palladium catalysts. J. Org. Chem. 68, 6767–6774 (2003).
    Article CAS Google Scholar
  25. Gartner, Z.J., Kanan, M.W. & Liu, D.R. Expanding the reaction scope of DNA-templated synthesis. Angew. Chem. Int. Ed. 41, 1796–1800 (2002).
    Article CAS Google Scholar

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Author notes

  1. Matthew A Clark, Raksha A Acharya, Christopher C Arico-Muendel, Svetlana L Belyanskaya, Dennis R Benjamin, Neil R Carlson, Paolo A Centrella, Cynthia H Chiu, Steffen P Creaser, John W Cuozzo, Christopher P Davie, Yun Ding, G Joseph Franklin, Kurt D Franzen, Malcolm L Gefter, Steven P Hale, Nils J V Hansen, David I Israel, Jinwei Jiang, Malcolm J Kavarana, Michael S Kelley, Christopher S Kollmann, Fan Li, Kenneth Lind, Sibongile Mataruse, Patricia F Medeiros, Jeffrey A Messer, Paul Myers, Heather O'Keefe, Matthew C Oliff, Cecil E Rise, Alexander L Satz, Steven R Skinner, Jennifer L Svendsen, Lujia Tang, Kurt van Vloten, Richard W Wagner, Gang Yao & Barry A Morgan
    Present address: Present addresses: GlaxoSmithKline, Molecular Discovery Research Boston, Waltham, Massachusetts, USA (M.A.C., C.C.A.-M., S.L.B., N.R.C., P.A.C., C.H.C., J.W.C., C.P.D., Y.D., G.J.F., D.I.I., M.S.K., C.S.K., K.L., P.F.M., J.A.M., H.O., C.E.R., A.L.S., S.R.S., G.Y. and B.A.M.); Bedford, Massachusetts, USA (R.A.A.); Seattle Genetics, Inc., Bothell, Washington, USA (D.R.B.); Satori Pharmaceuticals, Cambridge, Massachusetts, USA (S.P.C.); ParagonDx, LLC, Morrisville, North Carolina, USA (K.D.F.); Lincoln, Massachusetts, USA (M.L.G.); Ensemble Discovery Corporation, Cambridge, Massachusetts, USA (S.P.H.); Vipergen, Copenhagen, Denmark (N.J.V.H.); AVEO Pharmaceuticals, Inc., Cambridge, Massachusetts, USA (J.J.); Foley & Lardner LLP, Washington, DC, USA (M.J.K.); Medway, Massachusetts, USA (F.L.); Massachusetts College of Pharmacy and Health Sciences, Worcester, Massachusetts, USA (S.M. and J.L.S.); Monsanto, Cambridge, Massachusetts, USA (P.M.); Columbia University, College of Physicians and Surgeons, New York, New York, USA (M.C.O.); Novartis Pharmaceuticals, Cambridge, Massachusetts, USA (L.T.); Biogen IDEC, Cambridge, Massachusetts, USA (K.v.V.); SRU Biosystems, Woburn, Massachusetts, USA (R.W.W.).,

Authors and Affiliations

  1. The former Praecis Pharmaceuticals, Waltham, Massachusetts, USA, presently GlaxoSmithKline, Molecular Discovery Research Boston, Waltham, Massachusetts, USA
    Matthew A Clark, Raksha A Acharya, Christopher C Arico-Muendel, Svetlana L Belyanskaya, Dennis R Benjamin, Neil R Carlson, Paolo A Centrella, Cynthia H Chiu, Steffen P Creaser, John W Cuozzo, Christopher P Davie, Yun Ding, G Joseph Franklin, Kurt D Franzen, Malcolm L Gefter, Steven P Hale, Nils J V Hansen, David I Israel, Jinwei Jiang, Malcolm J Kavarana, Michael S Kelley, Christopher S Kollmann, Fan Li, Kenneth Lind, Sibongile Mataruse, Patricia F Medeiros, Jeffrey A Messer, Paul Myers, Heather O'Keefe, Matthew C Oliff, Cecil E Rise, Alexander L Satz, Steven R Skinner, Jennifer L Svendsen, Lujia Tang, Kurt van Vloten, Richard W Wagner, Gang Yao & Barry A Morgan
  2. GlaxoSmithKline, Computational and Structural Chemistry, King of Prussia, Pennsylvania, USA
    Baoguang Zhao

Authors

  1. Matthew A Clark
  2. Raksha A Acharya
  3. Christopher C Arico-Muendel
  4. Svetlana L Belyanskaya
  5. Dennis R Benjamin
  6. Neil R Carlson
  7. Paolo A Centrella
  8. Cynthia H Chiu
  9. Steffen P Creaser
  10. John W Cuozzo
  11. Christopher P Davie
  12. Yun Ding
  13. G Joseph Franklin
  14. Kurt D Franzen
  15. Malcolm L Gefter
  16. Steven P Hale
  17. Nils J V Hansen
  18. David I Israel
  19. Jinwei Jiang
  20. Malcolm J Kavarana
  21. Michael S Kelley
  22. Christopher S Kollmann
  23. Fan Li
  24. Kenneth Lind
  25. Sibongile Mataruse
  26. Patricia F Medeiros
  27. Jeffrey A Messer
  28. Paul Myers
  29. Heather O'Keefe
  30. Matthew C Oliff
  31. Cecil E Rise
  32. Alexander L Satz
  33. Steven R Skinner
  34. Jennifer L Svendsen
  35. Lujia Tang
  36. Kurt van Vloten
  37. Richard W Wagner
  38. Gang Yao
  39. Baoguang Zhao
  40. Barry A Morgan

Corresponding author

Correspondence toBarry A Morgan.

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Clark, M., Acharya, R., Arico-Muendel, C. et al. Design, synthesis and selection of DNA-encoded small-molecule libraries.Nat Chem Biol 5, 647–654 (2009). https://doi.org/10.1038/nchembio.211

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