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Journal articles on the topic 'DNA-encoded libraries'

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Author: Grafiati

Published: 10 December 2022

Last updated: 14 March 2023

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1

Dumelin, Christoph E, Jörg Scheuermann, Samu Melkko, and Dario Neri. "DNA-Encoded Chemical Libraries." QSAR & Combinatorial Science 25, no. 11 (November 2006): 1081–87. http://dx.doi.org/10.1002/qsar.200640104.

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2

Scheuermann, Jörg, Christoph E. Dumelin, Samu Melkko, and Dario Neri. "DNA-encoded chemical libraries." Journal of Biotechnology 126, no. 4 (December 2006): 568–81. http://dx.doi.org/10.1016/j.jbiotec.2006.05.018.

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3

Shi, Bingbing, Yu Zhou, and Xiaoyu Li. "Recent advances in DNA-encoded dynamic libraries." RSC Chemical Biology 3, no. 4 (2022): 407–19. http://dx.doi.org/10.1039/d2cb00007e.

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A brief review on the recent development of DNA-encoded dynamic libraries (DEDLs) is provided, highlighting their distinct features from traditional dynamic chemical libraries and static DNA-encoded libraries.

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4

Michael McCoy. "NovAliX invests in DNA-encoded libraries." C&EN Global Enterprise 98, no. 48 (December 21, 2020): 19. http://dx.doi.org/10.1021/cen-09848-buscon16.

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5

Franzini, Raphael M., and Cassie Randolph. "Chemical Space of DNA-Encoded Libraries." Journal of Medicinal Chemistry 59, no. 14 (February 25, 2016): 6629–44. http://dx.doi.org/10.1021/acs.jmedchem.5b01874.

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6

Connors, William H., Stephen P. Hale, and Nicholas K. Terrett. "DNA-encoded chemical libraries of macrocycles." Current Opinion in Chemical Biology 26 (June 2015): 42–47. http://dx.doi.org/10.1016/j.cbpa.2015.02.004.

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7

Scheuermann, Jörg, and Dario Neri. "Dual-pharmacophore DNA-encoded chemical libraries." Current Opinion in Chemical Biology 26 (June 2015): 99–103. http://dx.doi.org/10.1016/j.cbpa.2015.02.021.

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8

Reddavide, Francesco V., Weilin Lin, Sarah Lehnert, and Yixin Zhang. "DNA-Encoded Dynamic Combinatorial Chemical Libraries." Angewandte Chemie 127, no. 27 (May 26, 2015): 8035–39. http://dx.doi.org/10.1002/ange.201501775.

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9

Lerner, Richard A., and Dario Neri. "Reflections on DNA-encoded chemical libraries." Biochemical and Biophysical Research Communications 527, no. 3 (June 2020): 757–59. http://dx.doi.org/10.1016/j.bbrc.2020.04.080.

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10

Flood, Dillon T., Cian Kingston, Julien C. Vantourout, Philip E. Dawson, and Phil S. Baran. "DNA Encoded Libraries: A Visitor's Guide." Israel Journal of Chemistry 60, no. 3-4 (January 17, 2020): 268–80. http://dx.doi.org/10.1002/ijch.201900133.

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11

Reddavide, Francesco V., Weilin Lin, Sarah Lehnert, and Yixin Zhang. "DNA-Encoded Dynamic Combinatorial Chemical Libraries." Angewandte Chemie International Edition 54, no. 27 (May 26, 2015): 7924–28. http://dx.doi.org/10.1002/anie.201501775.

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12

Franzini, Raphael M., Dario Neri, and Jörg Scheuermann. "DNA-Encoded Chemical Libraries: Advancing beyond Conventional Small-Molecule Libraries." Accounts of Chemical Research 47, no. 4 (March 28, 2014): 1247–55. http://dx.doi.org/10.1021/ar400284t.

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13

Cai, Pinwen, Lukas A. Schneider, Cedric Stress, and Dennis Gillingham. "Building Boron Heterocycles into DNA-Encoded Libraries." Organic Letters 23, no. 22 (November 1, 2021): 8772–76. http://dx.doi.org/10.1021/acs.orglett.1c03262.

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14

Mannocci, Luca, Markus Leimbacher, Moreno Wichert, Jörg Scheuermann, and Dario Neri. "20 years of DNA-encoded chemical libraries." Chemical Communications 47, no. 48 (2011): 12747. http://dx.doi.org/10.1039/c1cc15634a.

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15

Buller, Fabian, Luca Mannocci, Jörg Scheuermann, and Dario Neri. "Drug Discovery with DNA-Encoded Chemical Libraries." Bioconjugate Chemistry 21, no. 9 (September 15, 2010): 1571–80. http://dx.doi.org/10.1021/bc1001483.

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16

Scheuermann, Jörg, and Dario Neri. "Special edition on DNA-Encoded chemical libraries." Biochemical and Biophysical Research Communications 533, no. 2 (December 2020): iii—iv. http://dx.doi.org/10.1016/j.bbrc.2020.10.055.

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17

Mullard, Asher. "DNA-encoded drug libraries come of age." Nature Biotechnology 34, no. 5 (May 2016): 450–51. http://dx.doi.org/10.1038/nbt0516-450b.

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18

MELKKO, S., C. DUMELIN, J. SCHEUERMANN, and D. NERI. "Lead discovery by DNA-encoded chemical libraries." Drug Discovery Today 12, no. 11-12 (June 2007): 465–71. http://dx.doi.org/10.1016/j.drudis.2007.04.007.

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19

Eidam, Oliv, and Alexander L. Satz. "Analysis of the productivity of DNA encoded libraries." MedChemComm 7, no. 7 (2016): 1323–31. http://dx.doi.org/10.1039/c6md00221h.

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Analysis of physical properties and structural diversity of 57 molecules derived from screening 5–16 DNA encoded libraries against two protein targets. DNA encoded library size is not predictive of productivity.

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20

Satz, Alexander Lee, Jianping Cai, Yi Chen, Robert Goodnow, Felix Gruber, Agnieszka Kowalczyk, Ann Petersen, Goli Naderi-Oboodi, Lucja Orzechowski, and Quentin Strebel. "DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries." Bioconjugate Chemistry 26, no. 8 (July 10, 2015): 1623–32. http://dx.doi.org/10.1021/acs.bioconjchem.5b00239.

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21

Dawadi, Surendra, Nicholas Simmons, Gabriella Miklossy, Kurt M. Bohren, John C. Faver, Melek Nihan Ucisik, Pranavanand Nyshadham, Zhifeng Yu, and Martin M. Matzuk. "Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library." Proceedings of the National Academy of Sciences 117, no. 29 (July 8, 2020): 16782–89. http://dx.doi.org/10.1073/pnas.2005447117.

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DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).

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22

Cao, Cheng, Peng Zhao, Ze Li, Zitian Chen, Yanyi Huang, Yu Bai, and Xiaoyu Li. "A DNA-templated synthesis of encoded small molecules by DNA self-assembly." Chem. Commun. 50, no. 75 (2014): 10997–99. http://dx.doi.org/10.1039/c4cc03380a.

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23

Plais, Louise, and Jörg Scheuermann. "Macrocyclic DNA-encoded chemical libraries: a historical perspective." RSC Chemical Biology 3, no. 1 (2022): 7–17. http://dx.doi.org/10.1039/d1cb00161b.

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DNA-encoded chemical libraries (DELs) have been used for the discovery of novel macrocyclic peptides for protein targets of interest. We review the reported macrocyclic DELs and discuss the achievements and challenges of this promising field.

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24

Reddavide, Francesco V., Meiying Cui, Weilin Lin, Naiqiang Fu, Stephan Heiden, Helena Andrade, Michael Thompson, and Yixin Zhang. "Second generation DNA-encoded dynamic combinatorial chemical libraries." Chemical Communications 55, no. 26 (2019): 3753–56. http://dx.doi.org/10.1039/c9cc01429b.

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25

Salamon, Hazem, Mateja Klika Škopić, Kathrin Jung, Olivia Bugain, and Andreas Brunschweiger. "Chemical Biology Probes from Advanced DNA-encoded Libraries." ACS Chemical Biology 11, no. 2 (January 28, 2016): 296–307. http://dx.doi.org/10.1021/acschembio.5b00981.

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26

Satz, Alexander L. "What Do You Get from DNA-Encoded Libraries?" ACS Medicinal Chemistry Letters 9, no. 5 (April 17, 2018): 408–10. http://dx.doi.org/10.1021/acsmedchemlett.8b00128.

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27

Ding, Yun, G. Joseph Franklin, Jennifer L. DeLorey, Paolo A. Centrella, Sibongile Mataruse, Matthew A. Clark, Steven R. Skinner, and Svetlana Belyanskaya. "Design and Synthesis of Biaryl DNA-Encoded Libraries." ACS Combinatorial Science 18, no. 10 (September 2016): 625–29. http://dx.doi.org/10.1021/acscombsci.6b00078.

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28

Samain, Florent, and Giulio Casi. "Small targeted cytotoxics from DNA-encoded chemical libraries." Current Opinion in Chemical Biology 26 (June 2015): 72–79. http://dx.doi.org/10.1016/j.cbpa.2015.02.009.

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29

Chan, Alix I., Lynn M. McGregor, and David R. Liu. "Novel selection methods for DNA-encoded chemical libraries." Current Opinion in Chemical Biology 26 (June 2015): 55–61. http://dx.doi.org/10.1016/j.cbpa.2015.02.010.

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30

Kleiner, Ralph E., Christoph E. Dumelin, and David R. Liu. "Small-molecule discovery from DNA-encoded chemical libraries." Chemical Society Reviews 40, no. 12 (2011): 5707. http://dx.doi.org/10.1039/c1cs15076f.

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31

Favalli, Nicholas, Gabriele Bassi, Jörg Scheuermann, and Dario Neri. "DNA-encoded chemical libraries - achievements and remaining challenges." FEBS Letters 592, no. 12 (May 10, 2018): 2168–80. http://dx.doi.org/10.1002/1873-3468.13068.

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32

Neri, Dario. "Twenty-five Years of DNA-Encoded Chemical Libraries." ChemBioChem 18, no. 9 (March 20, 2017): 827–28. http://dx.doi.org/10.1002/cbic.201700130.

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33

Kodadek, Thomas, Nicholas G. Paciaroni, Madeline Balzarini, and Paige Dickson. "Beyond protein binding: recent advances in screening DNA-encoded libraries." Chemical Communications 55, no. 89 (2019): 13330–41. http://dx.doi.org/10.1039/c9cc06256d.

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DNA-encoded libraries are usually screened against tagged proteins to identify ligands, but many other screening modalities either have been, or likely will be, developed that expand the utility of these libraries as a source of bioactive molecules.

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34

Potowski, Marco, Florian Losch, Elena Wünnemann, Janina K. Dahmen, Silvia Chines, and Andreas Brunschweiger. "Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions." Chemical Science 10, no. 45 (2019): 10481–92. http://dx.doi.org/10.1039/c9sc04708e.

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DNA-encoded compound libraries are widely used in drug discovery. Screening of catalysts for compatibility with solid phase-coupled DNA sequences guided the selection of encoded reactions, exemplified by a Zn(II)-mediated aza-Diels–Alder reaction.

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35

Kunig, Verena, Marco Potowski, Anne Gohla, and Andreas Brunschweiger. "DNA-encoded libraries – an efficient small molecule discovery technology for the biomedical sciences." Biological Chemistry 399, no. 7 (June 27, 2018): 691–710. http://dx.doi.org/10.1515/hsz-2018-0119.

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Abstract DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

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36

Li, Gang, Wenlu Zheng, Zitian Chen, Yu Zhou, Yu Liu, Junrui Yang, Yanyi Huang, and Xiaoyu Li. "Design, preparation, and selection of DNA-encoded dynamic libraries." Chemical Science 6, no. 12 (2015): 7097–104. http://dx.doi.org/10.1039/c5sc02467f.

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37

Hamada, Shohei. "Organic Synthesis for Diversity Expansion of DNA Encoded Libraries." Journal of Synthetic Organic Chemistry, Japan 78, no. 8 (August 1, 2020): 813–15. http://dx.doi.org/10.5059/yukigoseikyokaishi.78.813.

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38

Huang, Yiran, Yizhou Li, and Xiaoyu Li. "Strategies for developing DNA-encoded libraries beyond binding assays." Nature Chemistry 14, no. 2 (February 2022): 129–40. http://dx.doi.org/10.1038/s41557-021-00877-x.

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39

Sunkari, Yashoda Krishna, Vijay Kumar Siripuram, Thu-Lan Nguyen, and Marc Flajolet. "High-power screening (HPS) empowered by DNA-encoded libraries." Trends in Pharmacological Sciences 43, no. 1 (January 2022): 4–15. http://dx.doi.org/10.1016/j.tips.2021.10.008.

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40

Plais, Louise, Alice Lessing, Michelle Keller, Adriano Martinelli, Sebastian Oehler, Gabriele Bassi, Dario Neri, and Jörg Scheuermann. "Universal encoding of next generation DNA-encoded chemical libraries." Chemical Science 13, no. 4 (2022): 967–74. http://dx.doi.org/10.1039/d1sc05721a.

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Large Encoding Design (LED) allows for the construction of DNA-encoded chemical libraries (DELs) of unprecedented sizes and designs. LED was validated and compared with previous encoding systems for amplifiability and performance in test selections.

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41

Estévez, Amalia M., Felix Gruber, Alexander L. Satz, Rainer E. Martin, and Hans Peter Wessel. "A carbohydrate-derived trifunctional scaffold for DNA-encoded libraries." Tetrahedron: Asymmetry 28, no. 6 (June 2017): 837–42. http://dx.doi.org/10.1016/j.tetasy.2017.04.007.

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42

Clark, Matthew A. "Selecting chemicals: the emerging utility of DNA-encoded libraries." Current Opinion in Chemical Biology 14, no. 3 (June 2010): 396–403. http://dx.doi.org/10.1016/j.cbpa.2010.02.017.

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43

Mannocci, Luca, Markus Leimbacher, Moreno Wichert, Joerg Scheuermann, and Dario Neri. "ChemInform Abstract: 20 Years of DNA-Encoded Chemical Libraries." ChemInform 43, no. 11 (February 16, 2012): no. http://dx.doi.org/10.1002/chin.201211268.

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44

Goodnow Jr., Robert A., and Christopher P. Davie. "2015 First Boston Symposium of Encoded Library Platforms." MedChemComm 7, no. 7 (2016): 1268–70. http://dx.doi.org/10.1039/c6md90023b.

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45

Gao, Yuting, Guixian Zhao, Pengyang He, Gong Zhang, Yangfeng Li, and Yizhou Li. "DNA-Compatible Synthesis of α,β-Epoxyketones for DNA-Encoded Chemical Libraries." Bioconjugate Chemistry 33, no. 1 (December 20, 2021): 105–10. http://dx.doi.org/10.1021/acs.bioconjchem.1c00567.

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46

Satz, Alexander Lee, Jianping Cai, Yi Chen, Robert Goodnow, Felix Gruber, Agnieszka Kowalczyk, Ann Petersen, Goli Naderi-Oboodi, Lucja Orzechowski, and Quentin Strebel. "Correction to DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries." Bioconjugate Chemistry 27, no. 10 (September 19, 2016): 2580. http://dx.doi.org/10.1021/acs.bioconjchem.6b00185.

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47

Neri, Dario, and Richard A. Lerner. "DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information." Annual Review of Biochemistry 87, no. 1 (June 20, 2018): 479–502. http://dx.doi.org/10.1146/annurev-biochem-062917-012550.

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The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.

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48

Dickson, Paige, and Thomas Kodadek. "Chemical composition of DNA-encoded libraries, past present and future." Organic & Biomolecular Chemistry 17, no. 19 (2019): 4676–88. http://dx.doi.org/10.1039/c9ob00581a.

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49

Litovchick, Alexander, Xia Tian, Michael I. Monteiro, Kaitlyn M. Kennedy, Marie-Aude Guié, Paolo Centrella, Ying Zhang, Matthew A. Clark, and Anthony D. Keefe. "Novel Nucleic Acid Binding Small Molecules Discovered Using DNA-Encoded Chemistry." Molecules 24, no. 10 (May 27, 2019): 2026. http://dx.doi.org/10.3390/molecules24102026.

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Inspired by the many reported successful applications of DNA-encoded chemical libraries in drug discovery projects with protein targets, we decided to apply this platform to nucleic acid targets. We used a 120-billion-compound set of 33 distinct DNA-encoded chemical libraries and affinity-mediated selection to discover binders to a panel of DNA targets. Here, we report the successful discovery of small molecules that specifically interacted with DNA G-quartets, which are stable structural motifs found in G-rich regions of genomic DNA, including in the promoter regions of oncogenes. For this study, we chose the G-quartet sequence found in the c-myc promoter as a primary target. Compounds enriched using affinity-mediated selection against this target demonstrated high-affinity binding and high specificity over DNA sequences not containing G-quartet motifs. These compounds demonstrated a moderate ability to discriminate between different G-quartet motifs and also demonstrated activity in a cell-based assay, suggesting direct target engagement in the cell. DNA-encoded chemical libraries and affinity-mediated selection are uniquely suited to discover binders to targets that have no inherent activity outside of a cellular context, and they may also be of utility in other nucleic acid structural motifs.

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50

Oehler, Sebastian, Louise Plais, Gabriele Bassi, Dario Neri, and Jörg Scheuermann. "Modular assembly and encoding strategies for dual-display DNA-encoded chemical libraries." Chemical Communications 57, no. 92 (2021): 12289–92. http://dx.doi.org/10.1039/d1cc04306d.

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