Scheuermann, J.  et al.: 2024 Science of Synthesis, 2023/5: DNA-Encoded Libraries DOI: 10.1055/sos-SD-241-00223
DNA-Encoded Libraries

3.2.2.1 Encoded Self-Assembling (Dynamic) Chemical Libraries

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Book

Editors: Scheuermann, J. ; Li, Y.

Authors: Barluenga, S. ; Bassi, G. ; Brunschweiger, A. ; Cai, B. ; Cazzamalli, S. ; Chheda, P. ; Cui, M. ; Cui, W. ; Fang, X. ; Farrera-Soler, L. ; Favalli, N. ; Feng, J.; Foley, T. L. ; Franzini, R. M. ; Georgiev, T. ; Gillingham, D. ; Gloger, A. ; Graham, J. D. ; Granados, A. ; Heiden, S.; Hou, W. ; Huang, Y. ; Keefe, A. D. ; Krusemark, C. J. ; Li, X. ; Li, Y. ; Lin, W. ; Litovchick, A.; Liu, G. ; Lu, X. ; Lucaroni, L. ; Ma, P. ; Migliorini, F. ; Molander, G. A. ; Neri, D. ; Nie, Q. ; Oehler, S. ; Prati, L. ; Puglioli, S. ; Reddavide, F. V. ; Satz, A. L. ; Sauter, B. ; Scheuermann, J. ; Schuman, D.; Simmons, N. ; Stanway-Gordon, H. A. ; Su, W. ; Sun, J. ; Thompson, M.; Vummidi, B. R.; Wang, X. ; Wang, Y. ; Wang, Z. ; Waring, M. J. ; Willems, S.; Winssinger, N. ; Xia, B. ; Xiong, F. ; Xu, H. ; Xu, L. ; Yang, G. ; Zhang, G. ; Zhang, Y. ; Zhou, Y.

Title: DNA-Encoded Libraries

Print ISBN: 9783132455221; Online ISBN: 9783132437357; Book DOI: 10.1055/b000000342

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.

 
  • 1 Brenner S, Lerner RA. Proc. Natl. Acad. Sci. U. S. A. 1992; 89: 5381
  • 2 Melkko S, Scheuermann J, Dumelin CE, Neri D. Nat. Biotechnol. 2004; 22: 568
  • 3 Neri D, Melkko S. WO 03076943A1, 2003
  • 4 Dumelin CE, Scheuermann J, Melkko S, Neri D. Bioconjugate Chem. 2006; 17: 366
  • 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
  • 7 Decurtins W, Franzini RM, Neri D, Scheuermann J, Wichert M. EP 3083957B1, 2018
  • 8 Samain F, Gorre ÉMD, Millul J, Donckele EJ, Gironda-Martínez A. WO 2020128064A1, 2020
  • 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
  • 11 Sprinz KI, Tagore DM, Hamilton AD. Bioorg. Med. Chem. Lett. 2005; 15: 3908
  • 12 Li G, Zheng W, Chen Z, Zhou Y, Liu Y, Yang J, Huang Y, Li X. Chem. Sci. 2015; 6: 7097
  • 13 Reddavide FV, Lin W, Lehnert S, Zhang Y. Angew. Chem. Int. Ed. 2015; 54: 7924
  • 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
  • 17 Zhou Y, Peng J, Shen W, Li X. Biochem. Biophys. Res. Commun. 2020; 533: 215
  • 18 Zimmermann G, Li Y, Rieder U, Mattarella M, Neri D, Scheuermann J. ChemBioChem 2017; 18: 853
  • 19 Lin W, Reddavide FV, Uzunova V, Gür FN, Zhang Y. Anal. Chem. 2015; 87: 864
  • 20 Catalano M, Oehler S, Prati L, Favalli N, Bassi G, Scheuermann J, Neri D. Anal. Chem. 2020; 92: 10822
  • 21 Prati L, Bigatti M, Donckele EJ, Neri D, Samain F. Biochem. Biophys. Res. Commun. 2020; 533: 235
  • 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
  • 24 Zhuang C, Guan X, Ma H, Cong H, Zhang W, Miao Z. Eur. J. Med. Chem. 2019; 163: 883
  • 25 Cazzamalli S, Dal Corso A, Widmayer F, Neri D. J. Am. Chem. Soc. 2018; 140: 1617
  • 26 Srinivasarao M, Galliford CV, Low PS. Nat. Rev. Drug Discovery 2015; 14: 203
  • 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
  • 29 Cazzamalli S, Dal Corso A, Neri D. J. Controlled Release 2017; 246: 39
  • 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
  • 31 Prati L, Lucaroni L, Cazzamalli S, Neri D, Oehler S unpublished results
  • 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
  • 33 Gironda-Martínez A, Neri D, Samain F, Donckele EJ. Org. Lett. 2019; 21: 9555
  • 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
  • 36 Halpin DR, Lee JA, Wrenn SJ, Harbury PB. PLoS Biol. 2004; 2: e175
  • 37 Kashida H, Doi T, Sakakibara T, Hayashi T, Asanuma H. J. Am. Chem. Soc. 2013; 135: 7960
  • 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
  • 39 Desjardins P, Conklin D. J. Vis. Exp. 2010; e2565
  • 40 OligoCalc: Oligonucleotide Properties Calculator http://biotools.nubic.northwestern.edu/OligoCalc.html (accessed November 24, 2022).
  • 41 Holdgate GA, Anderson M, Edfeldt F, Geschwindner S. J. Struct. Biol. 2010; 172: 142
  • 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
  • 44 Moy FJ, Haraki K, Mobilio D, Walker G, Powers R, Tabei K, Tong H, Siegel MM. Anal. Chem. 2001; 73: 571
  • 45 Annis DA, Nickbarg E, Yang X, Ziebell MR, Whitehurst CE. Curr. Opin. Chem. Biol. 2007; 11: 518
  • 46 Cazzamalli S, Dal Corso A, Neri D. Mol. Cancer Ther. 2016; 15: 2926
  • 47 Neri D, Lerner RA. Annu. Rev. Biochem. 2018; 87: 479
  • 48 Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Angew. Chem. Int. Ed. 2018; 57: 17178
  • 49 Oehler S, Plais L, Bassi G, Neri D, Scheuermann J. Chem. Commun. (Cambridge) 2021; 57: 12289
  • 50 Plais L, Lessing A, Keller M, Martinelli A, Oehler S, Bassi G, Neri D, Scheuermann J. Chem. Sci. 2022; 13: 967