Literature DB >> 25723146

Novel selection methods for DNA-encoded chemical libraries.

Alix I Chan1, Lynn M McGregor1, David R Liu2.   

Abstract

Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 25723146      PMCID: PMC4475454          DOI: 10.1016/j.cbpa.2015.02.010

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  55 in total

1.  Reaction discovery enabled by DNA-templated synthesis and in vitro selection.

Authors:  Matthew W Kanan; Mary M Rozenman; Kaori Sakurai; Thomas M Snyder; David R Liu
Journal:  Nature       Date:  2004-09-30       Impact factor: 49.962

2.  Discovery of chemical reactions through multidimensional screening.

Authors:  Aaron B Beeler; Shun Su; Chris A Singleton; John A Porco
Journal:  J Am Chem Soc       Date:  2007-02-07       Impact factor: 15.419

3.  Multiplexed protein detection by proximity ligation for cancer biomarker validation.

Authors:  Simon Fredriksson; William Dixon; Hanlee Ji; Albert C Koong; Michael Mindrinos; Ronald W Davis
Journal:  Nat Methods       Date:  2007-03-18       Impact factor: 28.547

4.  Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library.

Authors:  Samu Melkko; Yixin Zhang; Christoph E Dumelin; Jörg Scheuermann; Dario Neri
Journal:  Angew Chem Int Ed Engl       Date:  2007       Impact factor: 15.336

5.  Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

Authors:  Liangcai Gu; Chao Li; John Aach; David E Hill; Marc Vidal; George M Church
Journal:  Nature       Date:  2014-09-21       Impact factor: 49.962

6.  Selection of DNA-encoded small molecule libraries against unmodified and non-immobilized protein targets.

Authors:  Peng Zhao; Zitian Chen; Yizhou Li; Dawei Sun; Yuan Gao; Yanyi Huang; Xiaoyu Li
Journal:  Angew Chem Int Ed Engl       Date:  2014-07-07       Impact factor: 15.336

7.  Terminal protection of small molecule-linked ssDNA for label-free and sensitive fluorescent detection of folate receptor.

Authors:  Yunying Xu; Bingying Jiang; Jiaqing Xie; Yun Xiang; Ruo Yuan; Yaqin Chai
Journal:  Talanta       Date:  2014-05-13       Impact factor: 6.057

8.  PNA-encoded synthesis (PES) of a 10 000-member hetero-glycoconjugate library and microarray analysis of diverse lectins.

Authors:  Alexandre Novoa; Takuya Machida; Sofia Barluenga; Anne Imberty; Nicolas Winssinger
Journal:  Chembiochem       Date:  2014-08-26       Impact factor: 3.164

9.  Direct observation of individual endogenous protein complexes in situ by proximity ligation.

Authors:  Ola Söderberg; Mats Gullberg; Malin Jarvius; Karin Ridderstråle; Karl-Johan Leuchowius; Jonas Jarvius; Kenneth Wester; Per Hydbring; Fuad Bahram; Lars-Gunnar Larsson; Ulf Landegren
Journal:  Nat Methods       Date:  2006-10-29       Impact factor: 28.547

10.  Using an in situ proximity ligation assay to systematically profile endogenous protein-protein interactions in a pathway network.

Authors:  Tzu-Chi Chen; Kuan-Ting Lin; Chun-Houh Chen; Sheng-An Lee; Pei-Ying Lee; Yu-Wen Liu; Yu-Lun Kuo; Feng-Sheng Wang; Jin-Mei Lai; Chi-Ying F Huang
Journal:  J Proteome Res       Date:  2014-10-09       Impact factor: 4.466

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  15 in total

Review 1.  DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges.

Authors:  Adrián Gironda-Martínez; Etienne J Donckele; Florent Samain; Dario Neri
Journal:  ACS Pharmacol Transl Sci       Date:  2021-06-14

2.  The In Situ Enzymatic Screening (ISES) Approach to Reaction Discovery and Catalyst Identification.

Authors:  Robert A Swyka; David B Berkowitz
Journal:  Curr Protoc Chem Biol       Date:  2017-12-14

Review 3.  Selective Modulation of Dynamic Protein Complexes.

Authors:  Julie M Garlick; Anna K Mapp
Journal:  Cell Chem Biol       Date:  2020-08-11       Impact factor: 8.116

Review 4.  DNA-encoded chemical libraries - achievements and remaining challenges.

Authors:  Nicholas Favalli; Gabriele Bassi; Jörg Scheuermann; Dario Neri
Journal:  FEBS Lett       Date:  2018-05-10       Impact factor: 4.124

5.  Hit-Validation Methodologies for Ligands Isolated from DNA-Encoded Chemical Libraries.

Authors:  Gunther Zimmermann; Yizhou Li; Ulrike Rieder; Martin Mattarella; Dario Neri; Jörg Scheuermann
Journal:  Chembiochem       Date:  2017-01-30       Impact factor: 3.164

6.  Robustness of In Vitro Selection Assays of DNA-Encoded Peptidomimetic Ligands to CBX7 and CBX8.

Authors:  Kyle E Denton; Sijie Wang; Michael C Gignac; Natalia Milosevich; Fraser Hof; Emily C Dykhuizen; Casey J Krusemark
Journal:  SLAS Discov       Date:  2018-01-08       Impact factor: 3.341

7.  Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity.

Authors:  Dana Al Sulaiman; Jason Y H Chang; Sylvain Ladame
Journal:  Angew Chem Int Ed Engl       Date:  2017-04-06       Impact factor: 15.336

8.  Design, preparation, and selection of DNA-encoded dynamic libraries.

Authors:  Gang Li; Wenlu Zheng; Zitian Chen; Yu Zhou; Yu Liu; Junrui Yang; Yanyi Huang; Xiaoyu Li
Journal:  Chem Sci       Date:  2015-09-11       Impact factor: 9.825

9.  Automated screening for small organic ligands using DNA-encoded chemical libraries.

Authors:  Willy Decurtins; Moreno Wichert; Raphael M Franzini; Fabian Buller; Michael A Stravs; Yixin Zhang; Dario Neri; Jörg Scheuermann
Journal:  Nat Protoc       Date:  2016-03-17       Impact factor: 13.491

10.  Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

Authors:  Dmitry L Usanov; Alix I Chan; Juan Pablo Maianti; David R Liu
Journal:  Nat Chem       Date:  2018-04-02       Impact factor: 24.427

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