3.2. 2.1 Encoded Self-Assembling (Dynamic) Chemical Libraries
Book
Editors: Scheuermann, J. ; Li, Y.
Title: DNA-Encoded Libraries
Print ISBN: 9783132455221; Online ISBN: 9783132437357; Book DOI: 10.1055/b000000342
1st edition © 2024. Thieme. All rights reserved.
Georg Thieme Verlag KG, Stuttgart
Subjects: Organic Chemistry
Science of Synthesis Reference Libraries
Parent publication
Title: Science of Synthesis
DOI: 10.1055/b-00000101
Series Editors: Fürstner, A. (Editor-in-Chief); Carreira, E. M.; Faul, M.; Kobayashi, S.; Koch, G.; Molander, G. A.; Nevado, C.; Trost, B. M.; You, S.-L.
Type: Multivolume Edition
Abstract
Encoded self-assembling chemical (ESAC) libraries consist of two independent sets of complementary single-stranded chemical libraries (named “sublibraries”) assembled by DNA hybridization. Various ESAC formats based on the incorporation of different numbers of building blocks (e.g., ESAC1+1, ESAC2+1), optionally cyclized (e.g., ESAC+), have been proposed. In the dynamic ESAC format, the use of short complementary DNA strands enables constant reshuffling of sublibraries, thus further enhancing the enrichment of target-binding building-block pairs during selections. In this chapter, a comprehensive review of the synthetic, analytical, and hit-validation procedures reported for ESAC libraries is presented. Examples of success stories involving the use of the ESAC technology in drug discovery are also discussed.
Key words
DNA-encoded libraries - affinity maturation - DEL synthesis - dual-pharmacophore DEL - drug discovery - encoded self-assembling (dynamic) chemical libraries (ESAC) - hit validation - single-stranded sublibraries- 5 Scheuermann J, Dumelin CE, Melkko S, Zhang Y, Mannocci L, Jaggi M, Sobek J, Neri D. Bioconjugate Chem. 2008; 19: 778
- 6 Wichert M, Krall N, Decurtins W, Franzini RM, Pretto F, Schneider P, Neri D, Scheuermann J. Nat. Chem. 2015; 7: 241
- 9 Zimmermann G, Rieder U, Bajic D, Vanetti S, Chaikuad A, Knapp S, Scheuermann J, Mattarella M, Neri D. Chem.–Eur. J. 2017; 23: 8152
- 10 Bassi G, Favalli N, Vuk M, Catalano M, Martinelli A, Trenner A, Porro A, Yang S, Tham CL, Moroglu M, Yue WW, Conway SJ, Vogt PK, Sartori AA, Scheuermann J, Neri D. Adv. Sci. (Weinheim, Ger.) 2020; 7: 2001 970
- 14 Zhou Y, Li C, Peng J, Xie L, Meng L, Li Q, Zhang J, Li XD, Li X, Huang X, Li X. J. Am. Chem. Soc. 2018; 140: 15859
- 15 Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Angew. Chem. Int. Ed. 2020; 59: 14965
- 16 Reddavide FV, Cui M, Lin W, Fu N, Heiden S, Andrade H, Thompson M, Zhang Y. Chem. Commun. (Cambridge) 2019; 55: 3753
- 20 Catalano M, Oehler S, Prati L, Favalli N, Bassi G, Scheuermann J, Neri D. Anal. Chem. 2020; 92: 10822
- 22 Favalli N, Bassi G, Pellegrino C, Millul J, De Luca R, Cazzamalli S, Yang S, Trenner A, Mozaffari NL, Myburgh R, Moroglu M, Conway SJ, Sartori AA, Manz MG, Lerner RA, Vogt PK, Scheuermann J, Neri D. Nat. Chem. 2021; 13: 540
- 23 Bigatti M, Dal Corso A, Vanetti S, Cazzamalli S, Rieder U, Scheuermann J, Neri D, Sladojevich F. ChemMedChem 2017; 12: 1748
- 27 Cazzamalli S, Ziffels B, Widmayer F, Murer P, Pellegrini G, Pretto F, Wulhfard S, Neri D. Clin. Cancer Res. 2018; 24: 3656
- 28 Kulterer OC, Pfaff S, Wadsak W, Garstka N, Remzi M, Vraka C, Nics L, Mitterhauser M, Bootz F, Cazzamalli S, Krall N, Neri D, Haug AR. J. Nucl. Med. 2021; 62: 360
- 30 Gironda-Martínez A, Gorre ÉMD, Prati L, Gosalbes J.-F, Dakhel S, Cazzamalli S, Samain F, Donckele EJ, Neri D. J. Med. Chem. 2021; 64: 17496
- 32 Sannino A, Gironda-Martínez A, Gorre ÉMD, Prati L, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. ACS Comb. Sci. 2020; 22: 204
- 34 Vummidi BR, Farrera-Soler L, Daguer J.-P, Dockerill M, Barluenga S, Winssinger N. Nat. Chem. 2022; 14: 141
- 35 Farrera-Soler L, Daguer J.-P, Raunft P, Barluenga S, Imberty A, Winssinger N. Bioorg. Med. Chem. 2020; 28: 115458
- 38 Oehler S, Catalano M, Scapozza I, Bigatti M, Bassi G, Favalli N, Mortensen MR, Samain F, Scheuermann J, Neri D. Chem.–Eur. J. 2021; 27: 8985
- 40 OligoCalc: Oligonucleotide Properties Calculator http://biotools.nubic.northwestern.edu/OligoCalc.html (accessed November 24, 2022).
- 42 Jerabek-Willemsen M, André T, Wanner R, Roth HM, Duhr S, Baaske P, Breitsprecher D. J. Mol. Struct. 2014; 1077: 101
- 43 Pellecchia M, Bertini I, Cowburn D, Dalvit C, Giralt E, Jahnke W, James TL, Homans SW, Kessler H, Luchinat C, Meyer B, Oschkinat H, Peng J, Schwalbe H, Siegal G. Nat. Rev. Drug Discovery 2008; 7: 738