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Zeitschriftenartikel zum Thema „DNA-Encoded Chemical Library“

Autor: Grafiati

Veröffentlicht am 30. Juni 2021

Zuletzt aktualisiert am 29. Juli 2025

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1

Dawadi, Surendra, Nicholas Simmons, Gabriella Miklossy, et al. "Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library." Proceedings of the National Academy of Sciences 117, no. 29 (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

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2

Onda, Yuichi, Gabriele Bassi, Abdullah Elsayed, et al. "A DNA‐Encoded Chemical Library Based on Peptide Macrocycles." Chemistry – A European Journal 27, no. 24 (2021): 7160–67. http://dx.doi.org/10.1002/chem.202005423.

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3

Reddavide, Francesco V., Meiying Cui, Weilin Lin, et al. "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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4

Dumelin, Christoph E., Jörg Scheuermann, Samu Melkko, and Dario Neri. "Selection of Streptavidin Binders from a DNA-Encoded Chemical Library." Bioconjugate Chemistry 17, no. 2 (2006): 366–70. http://dx.doi.org/10.1021/bc050282y.

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5

Faver, John C., Kevin Riehle, David R. Lancia, et al. "Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections." ACS Combinatorial Science 21, no. 2 (2019): 75–82. http://dx.doi.org/10.1021/acscombsci.8b00116.

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6

Stress, Cedric J., Basilius Sauter, Lukas A. Schneider, Timothy Sharpe, and Dennis Gillingham. "A DNA‐Encoded Chemical Library Incorporating Elements of Natural Macrocycles." Angewandte Chemie International Edition 58, no. 28 (2019): 9570–74. http://dx.doi.org/10.1002/anie.201902513.

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7

Edwards, Paul. "Design and synthesis of a novel DNA-encoded chemical library." Drug Discovery Today 15, no. 15-16 (2010): 690–91. http://dx.doi.org/10.1016/j.drudis.2010.06.013.

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8

Dumelin, Christoph E, Sabrina Trüssel, Fabian Buller, et al. "A Portable Albumin Binder from a DNA-Encoded Chemical Library." Angewandte Chemie International Edition 47, no. 17 (2008): 3196–201. http://dx.doi.org/10.1002/anie.200704936.

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9

Dumelin, Christoph E, Sabrina Trüssel, Fabian Buller, et al. "A Portable Albumin Binder from a DNA-Encoded Chemical Library." Angewandte Chemie 120, no. 17 (2008): 3240–45. http://dx.doi.org/10.1002/ange.200704936.

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10

Shi, Ying, Yan-ran Wu, Jian-qiang Yu, Wan-nian Zhang, and Chun-lin Zhuang. "DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output." RSC Advances 11, no. 4 (2021): 2359–76. http://dx.doi.org/10.1039/d0ra09889b.

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We summarize a series of novel DNA-compatible chemistry reactions for DNA-encoded chemical library (DEL) building blocks and analyse the druggability of screened hit molecules via DELs in the past five years.

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11

Holdaway, Jerrett, and Gunda I. Georg. "An emerging target for male contraception." Science 384, no. 6698 (2024): 849–50. http://dx.doi.org/10.1126/science.adp6432.

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12

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 (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 identific

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13

Guasch, Laura, Michael Reutlinger, Daniel Stoffler, and Moreno Wichert. "Augmenting Chemical Space with DNA-encoded Library Technology and Machine Learning." CHIMIA International Journal for Chemistry 75, no. 1 (2021): 105–7. http://dx.doi.org/10.2533/chimia.2021.105.

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14

Zhou, Yu, Chen Li, Jianzhao Peng, et al. "DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery." Journal of the American Chemical Society 140, no. 46 (2018): 15859–67. http://dx.doi.org/10.1021/jacs.8b09277.

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15

Ji, Yue, Dongliang Dai, Huadong Luo, et al. "C–S Coupling of DNA-Conjugated Aryl Iodides for DNA-Encoded Chemical Library Synthesis." Bioconjugate Chemistry 32, no. 4 (2021): 685–89. http://dx.doi.org/10.1021/acs.bioconjchem.1c00076.

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16

Keller, Michelle, Dimitar Petrov, Andreas Gloger, et al. "Highly pure DNA-encoded chemical libraries by dual-linker solid-phase synthesis." Science 384, no. 6701 (2024): 1259–65. http://dx.doi.org/10.1126/science.adn3412.

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The first drugs discovered using DNA-encoded chemical library (DEL) screens have entered late-stage clinical development. However, DEL technology as a whole still suffers from poor chemical purity resulting in suboptimal performance. In this work, we report a technique to overcome this issue through self-purifying release of the DEL after magnetic bead–based synthesis. Both the first and last building blocks of each assembled library member were linked to the beads by tethers that could be cleaved by mutually orthogonal chemistry. Sequential cleavage of the first and last tether, with washing

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17

Ottl, Johannes, Lukas Leder, Jonas V. Schaefer, and Christoph E. Dumelin. "Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery." Molecules 24, no. 8 (2019): 1629. http://dx.doi.org/10.3390/molecules24081629.

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The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library p

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18

Mannocci, Luca, Yixin Zhang, Jörg Scheuermann, et al. "High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries." Proceedings of the National Academy of Sciences 105, no. 46 (2008): 17670–75. http://dx.doi.org/10.1073/pnas.0805130105.

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DNA encoding facilitates the construction and screening of large chemical libraries. Here, we describe general strategies for the stepwise coupling of coding DNA fragments to nascent organic molecules throughout individual reaction steps as well as the first implementation of high-throughput sequencing for the identification and relative quantification of the library members. The methodology was exemplified in the construction of a DNA-encoded chemical library containing 4,000 compounds and in the discovery of binders to streptavidin, matrix metalloproteinase 3, and polyclonal human IgG.

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19

Franzini, Raphael M., Angela Nauer, Jörg Scheuermann, and Dario Neri. "Interrogating target-specificity by parallel screening of a DNA-encoded chemical library against closely related proteins." Chemical Communications 51, no. 38 (2015): 8014–16. http://dx.doi.org/10.1039/c5cc01230a.

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20

Melkko, Samu, Yixin Zhang, Christoph E Dumelin, Jörg Scheuermann, and Dario Neri. "Isolation of High-Affinity Trypsin Inhibitors from a DNA-Encoded Chemical Library." Angewandte Chemie 119, no. 25 (2007): 4755–58. http://dx.doi.org/10.1002/ange.200700654.

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21

Melkko, Samu, Yixin Zhang, Christoph E Dumelin, Jörg Scheuermann, and Dario Neri. "Isolation of High-Affinity Trypsin Inhibitors from a DNA-Encoded Chemical Library." Angewandte Chemie International Edition 46, no. 25 (2007): 4671–74. http://dx.doi.org/10.1002/anie.200700654.

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22

Gironda-Martínez, Adrián, Dario Neri, Florent Samain, and Etienne J. Donckele. "DNA-Compatible Diazo-Transfer Reaction in Aqueous Media Suitable for DNA-Encoded Chemical Library Synthesis." Organic Letters 21, no. 23 (2019): 9555–58. http://dx.doi.org/10.1021/acs.orglett.9b03726.

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23

Zhou, Yu, Jianzhao Peng, Wenyin Shen, and Xiaoyu Li. "Psoralen as an interstrand DNA crosslinker in the selection of DNA-Encoded dynamic chemical library." Biochemical and Biophysical Research Communications 533, no. 2 (2020): 215–22. http://dx.doi.org/10.1016/j.bbrc.2020.04.033.

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24

Zhang, Ying, Sana Bazzaz, Corey Bienstock, et al. "Abstract 3163: Discovery of highly selective ligands for the Bcl-2 family of proteins using DNA-encoded chemical libraries." Cancer Research 85, no. 8_Supplement_1 (2025): 3163. https://doi.org/10.1158/1538-7445.am2025-3163.

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DNA-encoded chemical library (DEL) technology enables the efficient screening of large collections of encoded compounds and has emerged as a powerful tool for hit identification. De Novo design and synthesis of non-traditional encoded libraries such as a reversible covalent compound library and beyond Lipinski’s rule of five (bRo5) macrocyclic (MC) libraries have significantly expanded the chemical space available for DEL screening, and further enhances the feasibility of discovering highly selective ligands for challenging oncology targets. We will present examples of affinity-based ligand di

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25

Ratnayake, Anokha S., Mark E. Flanagan, Timothy L. Foley, et al. "A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis." ACS Combinatorial Science 21, no. 10 (2019): 650–55. http://dx.doi.org/10.1021/acscombsci.9b00113.

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26

Yang, Guanyu, Dou He, Yijun Zhu, et al. "Cholesterol-Modified Oligonucleotides as Internal Reaction Controls during DNA-Encoded Chemical Library Synthesis." Bioconjugate Chemistry 32, no. 4 (2021): 667–71. http://dx.doi.org/10.1021/acs.bioconjchem.1c00045.

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27

Li, Jian-Yuan, Gabriella Miklossy, Ram K. Modukuri, et al. "Palladium-Catalyzed Hydroxycarbonylation of (Hetero)aryl Halides for DNA-Encoded Chemical Library Synthesis." Bioconjugate Chemistry 30, no. 8 (2019): 2209–15. http://dx.doi.org/10.1021/acs.bioconjchem.9b00447.

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28

Mannocci, Luca, Samu Melkko, Fabian Buller, et al. "Isolation of Potent and Specific Trypsin Inhibitors from a DNA-Encoded Chemical Library." Bioconjugate Chemistry 21, no. 10 (2010): 1836–41. http://dx.doi.org/10.1021/bc100198x.

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29

Shi, Bingbing, Yu Zhou, Yiran Huang, Jianfu Zhang, and Xiaoyu Li. "Recent advances on the encoding and selection methods of DNA-encoded chemical library." Bioorganic & Medicinal Chemistry Letters 27, no. 3 (2017): 361–69. http://dx.doi.org/10.1016/j.bmcl.2016.12.025.

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30

Leimbacher, Markus, Yixin Zhang, Luca Mannocci, et al. "Discovery of Small-Molecule Interleukin-2 Inhibitors from a DNA-Encoded Chemical Library." Chemistry - A European Journal 18, no. 25 (2012): 7729–37. http://dx.doi.org/10.1002/chem.201200952.

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31

Parandoosh, Z., S. K. Knowles, X. Y. Xiao, C. Zhao, G. S. David, and M. P. Nova. "Encoded chemical synthesis coupled to screening: "Pot Assay"." Combinatorial Chemistry & High Throughput Screening 1, no. 3 (1998): 135–42. http://dx.doi.org/10.2174/138620730103220120141950.

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A variety of screening methodologies is available to identify lead compounds. Screening methods that would permit the direct use of libraries made via the Radiofrequency Encoded Combinatorial chemistry paradigm (each individual small molecule in the library is presented separately on an individual encoded support) have the potential to diminish burdensome steps in this process. Here we report on our studies leading to such a direct method, which we have termed a Pot Assay. Pot Assay is a multiplex assay, which simultaneously measures specific binding of a number of ligands to at least one targ

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32

Chen, Ying-Chu, John C. Faver, Angela F. Ku, et al. "C–N Coupling of DNA-Conjugated (Hetero)aryl Bromides and Chlorides for DNA-Encoded Chemical Library Synthesis." Bioconjugate Chemistry 31, no. 3 (2020): 770–80. http://dx.doi.org/10.1021/acs.bioconjchem.9b00863.

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33

Buller, Fabian, Luca Mannocci, Yixin Zhang, Christoph E. Dumelin, Jörg Scheuermann, and Dario Neri. "Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions." Bioorganic & Medicinal Chemistry Letters 18, no. 22 (2008): 5926–31. http://dx.doi.org/10.1016/j.bmcl.2008.07.038.

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34

Lemke, Mike, Hannah Ravenscroft, Nicole J. Rueb, Dmitri Kireev, Dana Ferraris, and Raphael M. Franzini. "Integrating DNA-encoded chemical libraries with virtual combinatorial library screening: Optimizing a PARP10 inhibitor." Bioorganic & Medicinal Chemistry Letters 30, no. 19 (2020): 127464. http://dx.doi.org/10.1016/j.bmcl.2020.127464.

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35

Franzini, Raphael M., Torun Ekblad, Nan Zhong, et al. "Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library." Angewandte Chemie International Edition 54, no. 13 (2015): 3927–31. http://dx.doi.org/10.1002/anie.201410736.

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36

Franzini, Raphael M., Torun Ekblad, Nan Zhong, et al. "Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library." Angewandte Chemie 127, no. 13 (2015): 3999–4003. http://dx.doi.org/10.1002/ange.201410736.

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37

Palaniappan, Murugesan, Kurt M. Bohren, Yong Wang, Damian W. Young, Suzanne A. Fuqua, and Martin M. Matzuk. "Abstract P6-10-12: Discovery and Development of Next-Generation Estrogen Receptor Mutant Inhibitors using DNA-Encoded Chemical Library Screening." Cancer Research 83, no. 5_Supplement (2023): P6–10–12—P6–10–12. http://dx.doi.org/10.1158/1538-7445.sabcs22-p6-10-12.

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Abstract Background: Activating somatic ESR1 mutations Y537S and D538G occur more frequently in endocrine therapy-resistant metastatic breast cancer, which is associated with an aggressive phenotype and poor survival in breast cancer patients. These gain of function mutant receptors are constitutively active and allow resistance to first-line endocrine therapies. Therefore, the development of next-generation small molecule drugs targeting mutant estrogen receptor (ER) is an important priority. Here, we searched the small molecule inhibitors for Y537S and D538D ER mutants using DNA-encoded chem

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38

Keefe, Anthony D., Arrash J. Baghaie, Paolo A. Centrella, et al. "Abstract 3662: DNA-encoded chemical library screening and machine-learning for hit identification for WD40 repeat targets including oncology targets such as DCAF1, WDR5 and WDR12." Cancer Research 85, no. 8_Supplement_1 (2025): 3662. https://doi.org/10.1158/1538-7445.am2025-3662.

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Abstract Training machine-learned models using DNA-Encoded Chemical Library screening data “DEL-ML” and using these models to rank compounds in virtual catalogs has been successful for hit identification for a range of individual oncology targets including ER alpha and c-KIT [McCloskey et al 2020]. Here we describe the importance of library quality and diversity, protein quality, screen design, appropriate profile choice, training set preparation and evaluation, promiscuity labeling, chemical representations, modeling algorithms and their tuning in the context of a systematic target class-base

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39

Zhang, Ying, Anthony Keefe, and Matthew A. Clark. "Abstract 3091: Discovery of highly selective ligands with unique binding modes for challenging oncology targets using DNA-encoded chemical libraries." Cancer Research 84, no. 6_Supplement (2024): 3091. http://dx.doi.org/10.1158/1538-7445.am2024-3091.

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Abstract DNA-encoded chemical library (DEL) technology enables the efficient screening of large collections of encoded compounds and has emerged as a powerful tool for hit identification in recent years. The technology allows for the multiplexed interrogation of target-ligand binding interactions and results in DEL hits with unusual binding modes and desirable selectivity. This screening methodology is particularly effective for oncology targets. Examples of discovery of highly selective ligands for challenging oncology targets, including kinases, protein-protein interactions, and receptors, w

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40

Zhang, Ying, Anthony Keefe, Paolo Centrella, et al. "Abstract 5331: DNA-encoded macrocyclic compound libraries for challenging targets." Cancer Research 83, no. 7_Supplement (2023): 5331. http://dx.doi.org/10.1158/1538-7445.am2023-5331.

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Abstract Increasingly drug discovery programs require the development of orally available and cell permeable classes of drugs derived from the chemical space beyond Lipinski’s rule of 5 (bRO5). The chameleon-like physicochemical properties and differentiated binding modes of bRO5 compounds make them suitable starting points, especially for difficult-to-drug targets beyond traditional small molecule drug discovery. The synthesis of macrocyclic (MC) peptide DNA-Encoded Libraries (DEL) aligns with these efforts and has been an important addition to the rapidly growing field of DNA-encoded small m

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41

Disch, Jeremy S., Jennifer M. Duffy, Esther C. Y. Lee та ін. "Bispecific Estrogen Receptor α Degraders Incorporating Novel Binders Identified Using DNA-Encoded Chemical Library Screening". Journal of Medicinal Chemistry 64, № 8 (2021): 5049–66. http://dx.doi.org/10.1021/acs.jmedchem.1c00127.

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42

Yuen, Lik Hang, Srikanta Dana, Yu Liu, et al. "A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes." Journal of the American Chemical Society 141, no. 13 (2019): 5169–81. http://dx.doi.org/10.1021/jacs.8b08039.

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43

Samain, Florent, Torun Ekblad, Gediminas Mikutis, et al. "Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library." Journal of Medicinal Chemistry 58, no. 12 (2015): 5143–49. http://dx.doi.org/10.1021/acs.jmedchem.5b00432.

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44

Hall, Justin, Timothy L. Foley, Qiuxia Chen, et al. "A simple method for determining compound affinity and chemical yield from DNA-encoded library selections." Biochemical and Biophysical Research Communications 527, no. 1 (2020): 250–56. http://dx.doi.org/10.1016/j.bbrc.2020.04.024.

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45

Buller, Fabian, Yixin Zhang, Jörg Scheuermann, Juliane Schäfer, Peter Bühlmann, and Dario Neri. "Discovery of TNF Inhibitors from a DNA-Encoded Chemical Library based on Diels-Alder Cycloaddition." Chemistry & Biology 16, no. 10 (2009): 1075–86. http://dx.doi.org/10.1016/j.chembiol.2009.09.011.

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46

Zhu, Zhengrong, LaShadric C. Grady, Yun Ding, et al. "Development of a Selection Method for Discovering Irreversible (Covalent) Binders from a DNA-Encoded Library." SLAS DISCOVERY: Advancing the Science of Drug Discovery 24, no. 2 (2018): 169–74. http://dx.doi.org/10.1177/2472555218808454.

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DNA-encoded libraries (DELs) have been broadly applied to identify chemical probes for target validation and lead discovery. To date, the main application of the DEL platform has been the identification of reversible ligands using multiple rounds of affinity selection. Irreversible (covalent) inhibition offers a unique mechanism of action for drug discovery research. In this study, we report a developing method of identifying irreversible (covalent) ligands from DELs. The new method was validated by using 3C protease (3CP) and on-DNA irreversible tool compounds (rupintrivir derivatives) spiked

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47

Kuai, Letian, Thomas O’Keeffe, and Christopher Arico-Muendel. "Randomness in DNA Encoded Library Selection Data Can Be Modeled for More Reliable Enrichment Calculation." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 5 (2018): 405–16. http://dx.doi.org/10.1177/2472555218757718.

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DNA Encoded Libraries (DELs) use unique DNA sequences to tag each chemical warhead within a library mixture to enable deconvolution following affinity selection against a target protein. With next-generation sequencing, millions to billions of sequences can be read and counted to report binding events. This unprecedented capability has enabled researchers to synthesize and analyze numerically large chemical libraries. Despite the common perception that each library member undergoes a miniaturized affinity assay, selections with higher complexity libraries often produce results that are difficu

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48

Kim, Dongwook, Yixing Sun, Dan Xie, et al. "Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-Encoded Chemical Library." Molecules 24, no. 15 (2019): 2764. http://dx.doi.org/10.3390/molecules24152764.

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As aberrant activity of protein kinases is observed in many disease states, these enzymes are common targets for therapeutics and detection of activity levels. The development of non-natural protein kinase substrates offers an approach to protein substrate competitive inhibitors, a class of kinase inhibitors with promise for improved specificity. Also, kinase activity detection approaches would benefit from substrates with improved activity and specificity. Here, we apply a substrate-mediated selection to a peptidomimetic DNA-encoded chemical library for enrichment of molecules that can be pho

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49

Brown, Dean G., Giles A. Brown, Paolo Centrella, et al. "Agonists and Antagonists of Protease-Activated Receptor 2 Discovered within a DNA-Encoded Chemical Library Using Mutational Stabilization of the Target." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 5 (2018): 429–36. http://dx.doi.org/10.1177/2472555217749847.

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The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library.

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50

Ruff, Yves, Roberto Martinez, Xavier Pellé, et al. "An Amphiphilic Polymer-Supported Strategy Enables Chemical Transformations under Anhydrous Conditions for DNA-Encoded Library Synthesis." ACS Combinatorial Science 22, no. 3 (2020): 120–28. http://dx.doi.org/10.1021/acscombsci.9b00164.

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