Literature DB >> 29683493

DNA-encoded chemical libraries - achievements and remaining challenges.

Nicholas Favalli1, Gabriele Bassi1, Jörg Scheuermann1, Dario Neri1.   

Abstract

DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
© 2018 Federation of European Biochemical Societies.

Entities:  

Keywords:  zzm321990DNAzzm321990; DNA-encoded chemical libraries; combinatorial chemistry; drug discovery; high-throughput DNA sequencing

Mesh:

Substances:

Year:  2018        PMID: 29683493      PMCID: PMC6126621          DOI: 10.1002/1873-3468.13068

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  58 in total

1.  A general method for the covalent labeling of fusion proteins with small molecules in vivo.

Authors:  Antje Keppler; Susanne Gendreizig; Thomas Gronemeyer; Horst Pick; Horst Vogel; Kai Johnsson
Journal:  Nat Biotechnol       Date:  2002-12-09       Impact factor: 54.908

2.  High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries.

Authors:  Fabian Buller; Martina Steiner; Jörg Scheuermann; Luca Mannocci; Ina Nissen; Manuel Kohler; Christian Beisel; Dario Neri
Journal:  Bioorg Med Chem Lett       Date:  2010-05-20       Impact factor: 2.823

3.  Linkage of recognition and replication functions by assembling combinatorial antibody Fab libraries along phage surfaces.

Authors:  A S Kang; C F Barbas; K D Janda; S J Benkovic; R A Lerner
Journal:  Proc Natl Acad Sci U S A       Date:  1991-05-15       Impact factor: 11.205

4.  Identification of structure-activity relationships from screening a structurally compact DNA-encoded chemical library.

Authors:  Raphael M Franzini; Torun Ekblad; Nan Zhong; Moreno Wichert; Willy Decurtins; Angela Nauer; Mauro Zimmermann; Florent Samain; Jörg Scheuermann; Peter J Brown; Jonathan Hall; Susanne Gräslund; Herwig Schüler; Dario Neri
Journal:  Angew Chem Int Ed Engl       Date:  2015-02-03       Impact factor: 15.336

5.  DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

Authors:  Raphael M Franzini; Dario Neri; Jörg Scheuermann
Journal:  Acc Chem Res       Date:  2014-03-28       Impact factor: 22.384

6.  Impact of a Central Scaffold on the Binding Affinity of Fragment Pairs Isolated from DNA-Encoded Self-Assembling Chemical Libraries.

Authors:  Martina Bigatti; Alberto Dal Corso; Sara Vanetti; Samuele Cazzamalli; Ulrike Rieder; Jörg Scheuermann; Dario Neri; Filippo Sladojevich
Journal:  ChemMedChem       Date:  2017-10-20       Impact factor: 3.466

7.  Discovering Drugs with DNA-Encoded Library Technology: From Concept to Clinic with an Inhibitor of Soluble Epoxide Hydrolase.

Authors:  Svetlana L Belyanskaya; Yun Ding; James F Callahan; Aili L Lazaar; David I Israel
Journal:  Chembiochem       Date:  2017-03-24       Impact factor: 3.164

8.  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

9.  Encoded Library Synthesis Using Chemical Ligation and the Discovery of sEH Inhibitors from a 334-Million Member Library.

Authors:  Alexander Litovchick; Christoph E Dumelin; Sevan Habeshian; Diana Gikunju; Marie-Aude Guié; Paolo Centrella; Ying Zhang; Eric A Sigel; John W Cuozzo; Anthony D Keefe; Matthew A Clark
Journal:  Sci Rep       Date:  2015-06-10       Impact factor: 4.379

10.  A generic selection system for improved expression and thermostability of G protein-coupled receptors by directed evolution.

Authors:  Christoph Klenk; Janosch Ehrenmann; Marco Schütz; Andreas Plückthun
Journal:  Sci Rep       Date:  2016-02-18       Impact factor: 4.379

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  21 in total

1.  Multistep Synthesis of 1,2,4-Oxadiazoles via DNA-Conjugated Aryl Nitrile Substrates.

Authors:  Huang-Chi Du; Madison C Bangs; Nicholas Simmons; Martin M Matzuk
Journal:  Bioconjug Chem       Date:  2019-04-10       Impact factor: 4.774

2.  A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis.

Authors:  Anokha S Ratnayake; Mark E Flanagan; Timothy L Foley; Justin D Smith; Jillian G Johnson; Justin Bellenger; Justin I Montgomery; Brian M Paegel
Journal:  ACS Comb Sci       Date:  2019-09-06       Impact factor: 3.784

3.  Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications.

Authors:  Nicholas Favalli; Gabriele Bassi; Christian Pellegrino; Jacopo Millul; Roberto De Luca; Samuele Cazzamalli; Su Yang; Anika Trenner; Nour L Mozaffari; Renier Myburgh; Mustafa Moroglu; Stuart J Conway; Alessandro A Sartori; Markus G Manz; Richard A Lerner; Peter K Vogt; Jörg Scheuermann; Dario Neri
Journal:  Nat Chem       Date:  2021-04-08       Impact factor: 24.427

4.  DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules.

Authors:  Christopher J Gerry; Mathias J Wawer; Paul A Clemons; Stuart L Schreiber
Journal:  J Am Chem Soc       Date:  2019-06-25       Impact factor: 15.419

5.  Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format.

Authors:  Gabriele Bassi; Nicholas Favalli; Sebastian Oehler; Adriano Martinelli; Marco Catalano; Jörg Scheuermann; Dario Neri
Journal:  Biochem Biophys Res Commun       Date:  2020-05-05       Impact factor: 3.575

6.  RASS-Enabled S/P-C and S-N Bond Formation for DEL Synthesis.

Authors:  Dillon T Flood; Xuejing Zhang; Xiang Fu; Zhenxiang Zhao; Shota Asai; Brittany B Sanchez; Emily J Sturgell; Julien C Vantourout; Paul Richardson; Mark E Flanagan; David W Piotrowski; Dominik K Kölmel; Jinqiao Wan; Mei-Hsuan Tsai; Jason S Chen; Phil S Baran; Philip E Dawson
Journal:  Angew Chem Int Ed Engl       Date:  2020-03-11       Impact factor: 15.336

7.  Biocompatible SuFEx Click Chemistry: Thionyl Tetrafluoride (SOF4 )-Derived Connective Hubs for Bioconjugation to DNA and Proteins.

Authors:  Feng Liu; Hua Wang; Suhua Li; Grant A L Bare; Xuemin Chen; Chu Wang; John E Moses; Peng Wu; K Barry Sharpless
Journal:  Angew Chem Int Ed Engl       Date:  2019-05-08       Impact factor: 15.336

8.  Expanding the materials space of DNA via organic-phase ring-opening metathesis polymerization.

Authors:  Xuyu Tan; Hao Lu; Yehui Sun; Xiaoying Chen; Dali Wang; Fei Jia; Ke Zhang
Journal:  Chem       Date:  2019-04-22       Impact factor: 22.804

Review 9.  Rethinking drug design in the artificial intelligence era.

Authors:  Petra Schneider; W Patrick Walters; Alleyn T Plowright; Norman Sieroka; Jennifer Listgarten; Robert A Goodnow; Jasmin Fisher; Johanna M Jansen; José S Duca; Thomas S Rush; Matthias Zentgraf; John Edward Hill; Elizabeth Krutoholow; Matthias Kohler; Jeff Blaney; Kimito Funatsu; Chris Luebkemann; Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2019-12-04       Impact factor: 84.694

10.  Discovery of PqsE Thioesterase Inhibitors for Pseudomonas aeruginosa Using DNA-Encoded Small Molecule Library Screening.

Authors:  Julie S Valastyan; Michael R Tota; Isabelle R Taylor; Vasiliki Stergioula; Graham A B Hone; Chari D Smith; Brad R Henke; Kenneth G Carson; Bonnie L Bassler
Journal:  ACS Chem Biol       Date:  2020-01-10       Impact factor: 5.100

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