Literature DB >> 19648931

Design, synthesis and selection of DNA-encoded small-molecule libraries.

Matthew A Clark1, 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, Baoguang Zhao, Barry A Morgan.   

Abstract

Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a long-sought goal. We report the synthesis and interrogation of an 800-million-member DNA-encoded library in which small molecules are covalently attached to an encoding oligonucleotide. The library was assembled by a combination of chemical and enzymatic synthesis, and interrogated by affinity selection. We describe methods for the selection and deconvolution of the chemical display library, and the discovery of inhibitors for two enzymes: Aurora A kinase and p38 MAP kinase.

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Year:  2009        PMID: 19648931     DOI: 10.1038/nchembio.211

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  23 in total

Review 1.  DNA-templated organic synthesis: nature's strategy for controlling chemical reactivity applied to synthetic molecules.

Authors:  Xiaoyu Li; David R Liu
Journal:  Angew Chem Int Ed Engl       Date:  2004-09-20       Impact factor: 15.336

2.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

Authors:  C Tuerk; L Gold
Journal:  Science       Date:  1990-08-03       Impact factor: 47.728

3.  Synthetic ligands discovered by in vitro selection.

Authors:  S Jarrett Wrenn; Rebecca M Weisinger; David R Halpin; Pehr B Harbury
Journal:  J Am Chem Soc       Date:  2007-10-06       Impact factor: 15.419

4.  Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions.

Authors:  Fabian Buller; Luca Mannocci; Yixin Zhang; Christoph E Dumelin; Jörg Scheuermann; Dario Neri
Journal:  Bioorg Med Chem Lett       Date:  2008-07-15       Impact factor: 2.823

Review 5.  Unnatural RNA display libraries.

Authors:  Adam Frankel; Shuwei Li; Shelley R Starck; Richard W Roberts
Journal:  Curr Opin Struct Biol       Date:  2003-08       Impact factor: 6.809

6.  Expanding the reaction scope of DNA-templated synthesis.

Authors:  Zev J Gartner; Matthew W Kanan; David R Liu
Journal:  Angew Chem Int Ed Engl       Date:  2002-05-17       Impact factor: 15.336

Review 7.  Progress in the development of selective inhibitors of aurora kinases.

Authors:  Andrew A Mortlock; Nicholas J Keen; Frederic H Jung; Nicola M Heron; Kevin M Foote; Robert W Wilkinson; Stephen Green
Journal:  Curr Top Med Chem       Date:  2005       Impact factor: 3.295

8.  Efficient one-step Suzuki arylation of unprotected halonucleosides, using water-soluble palladium catalysts.

Authors:  Elizabeth C Western; Jonathan R Daft; Edward M Johnson; Peter M Gannett; Kevin H Shaughnessy
Journal:  J Org Chem       Date:  2003-08-22       Impact factor: 4.354

9.  DNA display III. Solid-phase organic synthesis on unprotected DNA.

Authors:  David R Halpin; Juanghae A Lee; S Jarrett Wrenn; Pehr B Harbury
Journal:  PLoS Biol       Date:  2004-06-22       Impact factor: 8.029

10.  VX-680, a potent and selective small-molecule inhibitor of the Aurora kinases, suppresses tumor growth in vivo.

Authors:  Elizabeth A Harrington; David Bebbington; Jeff Moore; Richele K Rasmussen; Abi O Ajose-Adeogun; Tomoko Nakayama; Joanne A Graham; Cecile Demur; Thierry Hercend; Anita Diu-Hercend; Michael Su; Julian M C Golec; Karen M Miller
Journal:  Nat Med       Date:  2004-02-22       Impact factor: 53.440

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  151 in total

Review 1.  Comprehensive survey of chemical libraries for drug discovery and chemical biology: 2009.

Authors:  Roland E Dolle; Bertrand Le Bourdonnec; Karin Worm; Guillermo A Morales; Craig J Thomas; Wei Zhang
Journal:  J Comb Chem       Date:  2010-10-05

2.  Celebrating synthesis.

Authors: 
Journal:  Nat Chem Biol       Date:  2011-11-15       Impact factor: 15.040

3.  Discovery of Potent and Selective Inhibitors for ADAMTS-4 through DNA-Encoded Library Technology (ELT).

Authors:  Yun Ding; Heather O'Keefe; Jennifer L DeLorey; David I Israel; Jeffrey A Messer; Cynthia H Chiu; Steven R Skinner; Rosalie E Matico; Monique F Murray-Thompson; Fan Li; Matthew A Clark; John W Cuozzo; Christopher Arico-Muendel; Barry A Morgan
Journal:  ACS Med Chem Lett       Date:  2015-07-07       Impact factor: 4.345

4.  Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library.

Authors:  Hongfeng Deng; Jingye Zhou; Flora S Sundersingh; Jennifer Summerfield; Don Somers; Jeffrey A Messer; Alexander L Satz; Nicolas Ancellin; Christopher C Arico-Muendel; Katie L Sargent Bedard; Arthur Beljean; Svetlana L Belyanskaya; Ryan Bingham; Sarah E Smith; Eric Boursier; Paul Carter; Paolo A Centrella; Matthew A Clark; Chun-Wa Chung; Christopher P Davie; Jennifer L Delorey; Yun Ding; G Joseph Franklin; LaShadric C Grady; Kenny Herry; Clare Hobbs; Christopher S Kollmann; Barry A Morgan; Laura J Pothier Kaushansky; Quan Zhou
Journal:  ACS Med Chem Lett       Date:  2015-07-21       Impact factor: 4.345

5.  DNA tags help the hunt for drugs.

Authors:  Asher Mullard
Journal:  Nature       Date:  2016-02-18       Impact factor: 49.962

6.  Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.

Authors:  Pei-Pei Kung; Patrick Bingham; Benjamin J Burke; Qiuxia Chen; Xuemin Cheng; Ya-Li Deng; Dengfeng Dou; Junli Feng; Gary M Gallego; Michael R Gehring; Stephan K Grant; Samantha Greasley; Anthony R Harris; Karen A Maegley; Jordan Meier; Xiaoyun Meng; Jose L Montano; Barry A Morgan; Brigitte S Naughton; Prakash B Palde; Thomas A Paul; Paul Richardson; Sylvie Sakata; Alex Shaginian; William K Sonnenburg; Chakrapani Subramanyam; Sergei Timofeevski; Jinqiao Wan; Wen Yan; Albert E Stewart
Journal:  ACS Med Chem Lett       Date:  2020-04-10       Impact factor: 4.345

7.  Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support.

Authors:  Dillon T Flood; Shota Asai; Xuejing Zhang; Jie Wang; Leonard Yoon; Zoë C Adams; Blythe C Dillingham; Brittany B Sanchez; Julien C Vantourout; Mark E Flanagan; David W Piotrowski; Paul Richardson; Samantha A Green; Ryan A Shenvi; Jason S Chen; Phil S Baran; Philip E Dawson
Journal:  J Am Chem Soc       Date:  2019-06-12       Impact factor: 15.419

8.  Solid-Phase Synthesis of β-Amino Ketones Via DNA-Compatible Organocatalytic Mannich Reactions.

Authors:  Nam Tran-Hoang; Thomas Kodadek
Journal:  ACS Comb Sci       Date:  2018-01-24       Impact factor: 3.784

9.  Screening one bead one compound libraries against serum using a flow cytometer: Determination of the minimum antibody concentration required for ligand discovery.

Authors:  Osayemwenre Erharuyi; Scott Simanski; Patrick J McEnaney; Thomas Kodadek
Journal:  Bioorg Med Chem Lett       Date:  2018-01-31       Impact factor: 2.823

10.  Cycloisomerization of Olefins in Water.

Authors:  Jeishla L M Matos; Samantha A Green; Yuge Chun; Vuong Q Dang; Russell G Dushin; Paul Richardson; Jason S Chen; David W Piotrowski; Brian M Paegel; Ryan A Shenvi
Journal:  Angew Chem Int Ed Engl       Date:  2020-05-28       Impact factor: 15.336

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