Design, synthesis and selection of DNA-encoded small-molecule libraries (original) (raw)
Accession codes
Accessions
Protein Data Bank
Change history
17 September 2009
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
- 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 - Barbas, C.F. III. Recent advances in phage display. Curr. Opin. Biotechnol. 4, 526–530 (1993).
Article CAS Google Scholar - 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 - 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 - 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 - Joyce, G.F. Amplification, mutation and selection of catalytic RNA. Gene 82, 83–87 (1989).
Article CAS Google Scholar - 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 - Brenner, S. & Lerner, R.A. Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89, 5381–5383 (1992).
Article CAS Google Scholar - 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 - 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 - 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 - 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 - Melkko, S., Scheurmann, J., Dumelin, C.E. & Neri, D. Encoded self-assembling chemical libraries. Nat. Biotechnol. 22, 568–574 (2004).
Article CAS Google Scholar - 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 - 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 - Morgan, B. et al. Synthesis of combinatorial libraries containing encoding oligonucleotide tags. WO patent application 2007/053358 (2007).
- 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).
- 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 - Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).
Article CAS Google Scholar - 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 - 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 - 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 - Burns, C.J., Wilks, A.F. & Bu, X. Preparation of pyrazine derivatives as kinase inhibitors. WO patent 2005/054230 (2005).
- 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 - 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
Author information
Author notes
- 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
- 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 - GlaxoSmithKline, Computational and Structural Chemistry, King of Prussia, Pennsylvania, USA
Baoguang Zhao
Authors
- Matthew A Clark
You can also search for this author inPubMed Google Scholar - Raksha A Acharya
You can also search for this author inPubMed Google Scholar - Christopher C Arico-Muendel
You can also search for this author inPubMed Google Scholar - Svetlana L Belyanskaya
You can also search for this author inPubMed Google Scholar - Dennis R Benjamin
You can also search for this author inPubMed Google Scholar - Neil R Carlson
You can also search for this author inPubMed Google Scholar - Paolo A Centrella
You can also search for this author inPubMed Google Scholar - Cynthia H Chiu
You can also search for this author inPubMed Google Scholar - Steffen P Creaser
You can also search for this author inPubMed Google Scholar - John W Cuozzo
You can also search for this author inPubMed Google Scholar - Christopher P Davie
You can also search for this author inPubMed Google Scholar - Yun Ding
You can also search for this author inPubMed Google Scholar - G Joseph Franklin
You can also search for this author inPubMed Google Scholar - Kurt D Franzen
You can also search for this author inPubMed Google Scholar - Malcolm L Gefter
You can also search for this author inPubMed Google Scholar - Steven P Hale
You can also search for this author inPubMed Google Scholar - Nils J V Hansen
You can also search for this author inPubMed Google Scholar - David I Israel
You can also search for this author inPubMed Google Scholar - Jinwei Jiang
You can also search for this author inPubMed Google Scholar - Malcolm J Kavarana
You can also search for this author inPubMed Google Scholar - Michael S Kelley
You can also search for this author inPubMed Google Scholar - Christopher S Kollmann
You can also search for this author inPubMed Google Scholar - Fan Li
You can also search for this author inPubMed Google Scholar - Kenneth Lind
You can also search for this author inPubMed Google Scholar - Sibongile Mataruse
You can also search for this author inPubMed Google Scholar - Patricia F Medeiros
You can also search for this author inPubMed Google Scholar - Jeffrey A Messer
You can also search for this author inPubMed Google Scholar - Paul Myers
You can also search for this author inPubMed Google Scholar - Heather O'Keefe
You can also search for this author inPubMed Google Scholar - Matthew C Oliff
You can also search for this author inPubMed Google Scholar - Cecil E Rise
You can also search for this author inPubMed Google Scholar - Alexander L Satz
You can also search for this author inPubMed Google Scholar - Steven R Skinner
You can also search for this author inPubMed Google Scholar - Jennifer L Svendsen
You can also search for this author inPubMed Google Scholar - Lujia Tang
You can also search for this author inPubMed Google Scholar - Kurt van Vloten
You can also search for this author inPubMed Google Scholar - Richard W Wagner
You can also search for this author inPubMed Google Scholar - Gang Yao
You can also search for this author inPubMed Google Scholar - Baoguang Zhao
You can also search for this author inPubMed Google Scholar - Barry A Morgan
You can also search for this author inPubMed Google Scholar
Corresponding author
Correspondence toBarry A Morgan.
Supplementary information
Rights and permissions
About this article
Cite this article
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
- Received: 20 November 2008
- Accepted: 18 June 2009
- Published: 02 August 2009
- Issue Date: September 2009
- DOI: https://doi.org/10.1038/nchembio.211