PDF herunterladen
Scheuermann, J.  et al.: 2024 Science of Synthesis, 2023/5: DNA-Encoded Libraries DOI: 10.1055/sos-SD-241-00285
DNA-Encoded Libraries

4.1 Selections by Affinity Capture on Solid Support

Weitere Informationen

Buch

Herausgeber: Scheuermann, J. ; Li, Y. 

Autoren: 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. 

Titel: DNA-Encoded Libraries

Print ISBN: 9783132455221; Online ISBN: 9783132437357; Buch-DOI: 10.1055/b000000342

1st edition © 2024. Thieme. All rights reserved.
Georg Thieme Verlag KG, Stuttgart

Fachgebiete: Organische Chemie

Science of Synthesis Reference Libraries



Übergeordnete Publikation

Titel: Science of Synthesis

DOI: 10.1055/b-00000101

Reihenherausgeber: 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.

Typ: Mehrbändiges Werk

Auch verfügbar auf
 


Abstract

DNA-encoded library (DEL) selection is the crucial step of separating DEL members with the desired binding properties for a protein target from the vast majority of DEL members that do not bind. This chapter focuses on what could be described as “classical DEL selections”: affinity-based selections of in-solution DELs against single, purified target proteins, which represent the vast majority of DEL selections now performed in industry and academia. This review discusses the pros and cons of key parameters for successful selections: the solid support used for immobilization of the protein targets, the affinity tags, and the input amount of DEL required, and includes representative experimental procedures for DEL selections on solid supports.

Schlüsselwörter

DNA-encoded libraries (DELs) - selection - solid supports - affinity tags - protein targets - screening - drug discovery - hit identification
 
  • 1 Satz AL, Brunschweiger A, Flanagan ME, Gloger A, Hansen NJV, Kuai L, Kunig VBK, Lu X, Madsen D, Marcaurelle LA, Mulrooney C, OʼDonovan G, Sakata S, Scheuermann J. Nat. Rev. Methods Primers 2022; 2: 3
  • 2 Melkko S, Scheuermann J, Dumelin CE, Neri D. Nat. Biotechnol. 2004; 22: 568
    PubMed
  • 3 Gartner ZJ, Tse BN, Grubina R, Doyon JB, Snyder TM, Liu DR. Science (Washington, D. C.) 2004; 305: 1601
    PubMed
  • 4 Mayr LM, Bojanic D. Curr. Opin. Pharmacol. 2009; 9: 580
    PubMed
  • 5 Ge R, Shen Z, Yin J, Chen W, Zhang Q, An Y, Tang D, Satz AL, Su W, Kuai L. SLAS Discovery 2022; 27: 79
    PubMed
  • 6 Cai B, Kim D, Akhand S, Sun Y, Cassell RJ, Alpsoy A, Dykhuizen EC, Van Rijn RM, Wendt MK, Krusemark CJ. J. Am. Chem. Soc. 2019; 141: 17057
    PubMed
  • 7 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
    PubMed
  • 8 Petersen LK, Christensen AB, Andersen J, Folkesson CG, Kristensen O, Andersen C, Alzu A, Sløk FA, Blakskjær P, Madsen D, Azevedo C, Micco I, Hansen NJV. J. Am. Chem. Soc. 2021; 143: 2751
    PubMed
  • 9 Cochrane WG, Malone ML, Dang VQ, Cavett V, Satz AL, Paegel BM. ACS Comb. Sci. 2019; 21: 425
    PubMed
  • 10 Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Angew. Chem. Int. Ed. 2018; 57: 17178
    PubMed
  • 11 McGregor LM, Jain T, Liu DR. J. Am. Chem. Soc. 2014; 136: 3264
    PubMed
  • 12 Huang Y, Meng L, Nie Q, Zhou Y, Chen L, Yang S, Fung YME, Li X, Huang C, Cao Y, Li Y, Li X. Nat. Chem. 2021; 13: 77
    PubMed
  • 13 Huang Y, Li Y, Li X. Nat. Chem. 2022; 14: 129
    PubMed
  • 14 Chamakuri S, Lu S, Ucisik MN, Bohren KM, Chen Y.-C, Du H.-C, Faver JC, Jimmidi R, Li F, Li J.-Y, Nyshadham P, Palmer SS, Pollet J, Qin X, Ronca SE, Sankaran B, Sharma KL, Tan Z, Versteeg L, Yu Z, Matzuk MM, Palzkill T, Young DW. Proc. Natl. Acad. Sci. U. S. A. 2021; 118: e2 111 172 118
  • 15 Ahn S, Kahsai AW, Pani B, Wang Q.-T, Zhao S, Wall AL, Strachan RT, Staus DP, Wingler LM, Sun LD, Sinnaeve J, Choi M, Cho T, Xu TT, Hansen GM, Burnett MB, Lamerdin JE, Bassoni DL, Gavino BJ, Husemoen G, Olsen EK, Franch T, Costanzi S, Chen X, Lefkowitz RJ. Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 1708
    PubMed
  • 16 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
    PubMed
  • 17 Machutta CA, Kollmann CS, Lind KE, Bai X, Chan PF, Huang J, Ballell L, Belyanskaya S, Besra GS, Barros-Aguirre D, Bates RH, Centrella PA, Chang SS, Chai J, Choudhry AE, Coffin A, Davie CP, Deng H, Deng J, Ding Y, Dodson JW, Fosbenner DT, Gao EN, Graham TL, Graybill TL, Ingraham K, Johnson WP, King BW, Kwiatkowski CR, Lelièvre J, Li Y, Liu X, Lu Q, Lehr R, Mendoza-Losana A, Martin J, McCloskey L, McCormick P, OʼKeefe HP, OʼKeeffe T, Pao C, Phelps CB, Qi H, Rafferty K, Scavello GS, Steiginga MS, Sundersingh FS, Sweitzer SM, Szewczuk LM, Taylor A, Toh MF, Wang J, Wang M, Wilkins DJ, Xia B, Yao G, Zhang J, Zhou J, Donahue CP, Messer JA, Holmes D, Arico-Muendel CC, Pope AJ, Gross JW, Evindar G. Nat. Commun. 2017; 8: 16081
    PubMed
  • 18 Su W, Ge R, Ding D, Chen W, Wang W, Yan H, Wang W, Yuan Y, Liu H, Zhang M, Zhang J, Shu Q, Satz AL, Kuai L. Bioconjugate Chem. 2021; 32: 1001
    PubMed
  • 19 Smith C. Nat. Methods 2005; 2: 71
  • 20 Teschner D, Wenzel G, Distler E, Schnürer E, Theobald M, Neurauter AA, Schjetne K, Herr W. Scand. J. Immunol. 2011; 74: 155
  • 21 Öhrfelt A, Brinkmalm A, Dumurgier J, Brinkmalm G, Hansson O, Zetterberg H, Bouaziz-Amar E, Hugon J, Paquet C, Blennow K. Alzheimerʼs Res. Ther. 2016; 8: 41
    PubMed
  • 22 Smith GP. Science (Washington, D. C.) 1985; 228: 1315
    PubMed
  • 23 Boder ET, Wittrup KD. Nat. Biotechnol. 1997; 15: 553
    PubMed
  • 24 Roberts RW, Szostak JW. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 12297
    PubMed
  • 25 Kleiner RE, Dumelin CE, Tiu GC, Sakurai K, Liu DR. J. Am. Chem. Soc. 2010; 132: 11779
    PubMed
  • 26 Porath J, Carlsson J, Olsson I, Belfrage G. Nature (London) 1975; 258: 598
    PubMed
  • 27 Hochuli E, Bannwarth W, Döbeli H, Gentz R, Stüber D. Nat. Biotechnol. 1988; 6: 1321
  • 28 Khan F, He M, Taussig MJ. Anal. Chem. 2006; 78: 3072
    PubMed
  • 29 Smith DB, Johnson KS. Gene 1988; 67: 31
    PubMed
  • 30 Fairhead M, Howarth M, In: Site-Specific Protein Labeling: Methods and Protocols Gautier A, Hinner MJ. Springer New York 2015; 1266. 171
    Crossref
  • 31 Heitzmann H, Richards FM. Proc. Natl. Acad. Sci. U. S. A. 1974; 71: 3537
    PubMed
  • 32 Keefe AD, Wilson DS, Seelig B, Szostak JW. Protein Expression Purif. 2001; 23: 440
    PubMed
  • 33 Schmidt TGM, Skerra A. Nat. Protoc. 2007; 2: 1528
    PubMed
  • 34 Schmidt TGM, Batz L, Bonet L, Carl U, Holzapfel G, Kiem K, Matulewicz K, Niermeier D, Schuchardt I, Stanar K. Protein Expression Purif. 2013; 92: 54
    PubMed
  • 35 Hopp TP, Prickett KS, Price VL, Libby RT, March CJ, Cerretti DP, Urdal DL, Conlon PJ. Nat. Biotechnol. 1988; 6: 1204
  • 36 Field J, Nikawa J.-I, Broek D, MacDonald B, Rodgers L, Wilson IA, Lerner RA, Wigler M. Mol. Cell. Biol. 1988; 8: 2159
    PubMed
  • 37 Evan GI, Lewis GK, Ramsay G, Bishop JM. Mol. Cell. Biol. 1985; 5: 3610
    PubMed
  • 38 Chatterjee DK, Esposito D. Protein Expression Purif. 2006; 46: 122
    PubMed
  • 39 Molday LL, Molday RS, In: Protein Affinity Tags: Methods and Protocols Giannone RJ, Dykstra AB. Springer New York 2014; 1177. 1
  • 40 Capon DJ, Chamow SM, Mordenti J, Marsters SA, Gregory T, Mitsuya H, Byrn RA, Lucas C, Wurm FM, Groopman JE, Broder S, Smith DH. Nature (London) 1989; 337: 525
    PubMed
  • 41 Götzke H, Kilisch M, Martínez-Carranza M, Sograte-Idrissi S, Rajavel A, Schlichthaerle T, Engels N, Jungmann R, Stenmark P, Opazo F, Frey S. Nat. Commun. 2019; 10: 4403
    PubMed
  • 42 Wichert M, Krall N, Decurtins W, Franzini RM, Pretto F, Schneider P, Neri D, Scheuermann J. Nat. Chem. 2015; 7: 241
    PubMed
  • 43 Melkko S, Dumelin CE, Scheuermann J, Neri D. Chem. Biol. 2006; 13: 225
    PubMed
  • 44 Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. ChemBioChem 2019; 20: 955
    PubMed
  • 45 Satz AL, Hochstrasser R, Petersen AC. ACS Comb. Sci. 2017; 19: 234
    PubMed
  • 46 Chen Q, Cheng X, Zhang L, Li X, Chen P, Liu J, Zhang L, Wei H, Li Z, Dou D. SLAS Discovery 2020; 25: 523
    PubMed
  • 47 Decurtins W, Wichert M, Franzini RM, Buller F, Stravs MA, Zhang Y, Neri D, Scheuermann J. Nat. Protoc. 2016; 11: 764
    PubMed
  • 48 Clark MA, Acharya RA, Arico-Muendel CC, Belyanskaya SL, Benjamin DR, Carlson NR, Centrella PA, Chiu CH, Creaser SP, Cuozzo JW, Davie CP, Ding Y, Franklin GJ, Franzen KD, Gefter ML, Hale SP, Hansen NJV, Israel DI, Jiang J, Kavarana MJ, Kelley MS, Kollmann CS, Li F, Lind K, Mataruse S, Medeiros PF, Messer JA, Myers P, OʼKeefe H, Oliff MC, Rise CE, Satz AL, Skinner SR, Svendsen JL, Tang L, van Vloten K, Wagner RW, Yao G, Zhao B, Morgan BA. Nat. Chem. Biol. 2009; 5: 647
    PubMed
  • 49 Kollmann CS, Bai X, Tsai C.-H, Yang H, Lind KE, Skinner SR, Zhu Z, Israel DI, Cuozzo JW, Morgan BA, Yuki K, Xie C, Springer TA, Shimaoka M, Evindar G. Bioorg. Med. Chem. 2014; 22: 2353
    PubMed