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Journal articles on the topic 'DNA Encoded Library'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Hackler, Amber L., Forrest G. FitzGerald, Vuong Q. Dang, Alexander L. Satz, and Brian M. Paegel. "Off-DNA DNA-Encoded Library Affinity Screening." ACS Combinatorial Science 22, no. 1 (December 12, 2019): 25–34. http://dx.doi.org/10.1021/acscombsci.9b00153.

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2

Brunschweiger, Andreas. "A DNA-encoded library special issue." Bioorganic & Medicinal Chemistry 56 (February 2022): 116582. http://dx.doi.org/10.1016/j.bmc.2021.116582.

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3

Cochrane, Wesley G., Marie L. Malone, Vuong Q. Dang, Valerie Cavett, Alexander L. Satz, and Brian M. Paegel. "Activity-Based DNA-Encoded Library Screening." ACS Combinatorial Science 21, no. 5 (March 18, 2019): 425–35. http://dx.doi.org/10.1021/acscombsci.9b00037.

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4

Zhang, Y., and M. A. Clark. "Design concepts for DNA-encoded library synthesis." Bioorganic & Medicinal Chemistry 41 (July 2021): 116189. http://dx.doi.org/10.1016/j.bmc.2021.116189.

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5

Shin, Min Hyeon, Kang Ju Lee, and Hyun-Suk Lim. "DNA-Encoded Combinatorial Library of Macrocyclic Peptoids." Bioconjugate Chemistry 30, no. 11 (October 30, 2019): 2931–38. http://dx.doi.org/10.1021/acs.bioconjchem.9b00628.

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6

Cochrane, Wesley G., Patrick R. Fitzgerald, and Brian M. Paegel. "Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening." ACS Chemical Biology 16, no. 12 (November 20, 2021): 2752–56. http://dx.doi.org/10.1021/acschembio.1c00714.

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7

Shen, Yurong, Guanyu Yang, Wei Huang, Alex Shaginian, Qian Lin, Jinqiao Wan, Jin Li, Yun Deng, and Guansai Liu. "Photoredox Deaminative Alkylation in DNA-Encoded Library Synthesis." Organic Letters 24, no. 14 (April 1, 2022): 2650–54. http://dx.doi.org/10.1021/acs.orglett.2c00697.

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8

Kómár, Péter, and Marko Kalinić. "Denoising DNA Encoded Library Screens with Sparse Learning." ACS Combinatorial Science 22, no. 8 (June 12, 2020): 410–21. http://dx.doi.org/10.1021/acscombsci.0c00007.

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9

Ding, Yun, Jing Chai, Paolo A. Centrella, Chenaimwoyo Gondo, Jennifer L. DeLorey, and Matthew A. Clark. "Development and Synthesis of DNA-Encoded Benzimidazole Library." ACS Combinatorial Science 20, no. 5 (April 12, 2018): 251–55. http://dx.doi.org/10.1021/acscombsci.8b00009.

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10

Onda, Yuichi, Gabriele Bassi, Abdullah Elsayed, Franziska Ulrich, Sebastian Oehler, Louise Plais, Jörg Scheuermann, and Dario Neri. "A DNA‐Encoded Chemical Library Based on Peptide Macrocycles." Chemistry – A European Journal 27, no. 24 (March 18, 2021): 7160–67. http://dx.doi.org/10.1002/chem.202005423.

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11

Goodnow, Robert. "DNA-Encoded Library Technology (DELT) After a Quarter Century." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 5 (May 21, 2018): 385–86. http://dx.doi.org/10.1177/2472555218766250.

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12

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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13

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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14

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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15

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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16

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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17

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 (March 2006): 366–70. http://dx.doi.org/10.1021/bc050282y.

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18

Satz, Alexander L. "DNA Encoded Library Selections and Insights Provided by Computational Simulations." ACS Chemical Biology 10, no. 10 (July 27, 2015): 2237–45. http://dx.doi.org/10.1021/acschembio.5b00378.

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19

Zhu, Zhengrong, Alex Shaginian, LaShadric C. Grady, Thomas O’Keeffe, Xiangguo E. Shi, Christopher P. Davie, Graham L. Simpson, et al. "Design and Application of a DNA-Encoded Macrocyclic Peptide Library." ACS Chemical Biology 13, no. 1 (December 4, 2017): 53–59. http://dx.doi.org/10.1021/acschembio.7b00852.

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20

Faver, John C., Kevin Riehle, David R. Lancia, Jared B. J. Milbank, Christopher S. Kollmann, Nicholas Simmons, Zhifeng Yu, and Martin M. Matzuk. "Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections." ACS Combinatorial Science 21, no. 2 (January 23, 2019): 75–82. http://dx.doi.org/10.1021/acscombsci.8b00116.

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21

Dumelin, Christoph E, Sabrina Trüssel, Fabian Buller, Eveline Trachsel, Frank Bootz, Yixin Zhang, Luca Mannocci, et al. "A Portable Albumin Binder from a DNA-Encoded Chemical Library." Angewandte Chemie 120, no. 17 (April 14, 2008): 3240–45. http://dx.doi.org/10.1002/ange.200704936.

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22

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 (July 8, 2019): 9570–74. http://dx.doi.org/10.1002/anie.201902513.

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23

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

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24

Dumelin, Christoph E, Sabrina Trüssel, Fabian Buller, Eveline Trachsel, Frank Bootz, Yixin Zhang, Luca Mannocci, et al. "A Portable Albumin Binder from a DNA-Encoded Chemical Library." Angewandte Chemie International Edition 47, no. 17 (April 14, 2008): 3196–201. http://dx.doi.org/10.1002/anie.200704936.

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25

Price, Alexander K., and Brian M. Paegel. "Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis." ACS Combinatorial Science 22, no. 11 (August 6, 2020): 649–55. http://dx.doi.org/10.1021/acscombsci.0c00101.

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26

Xia, Bing, G. Joseph Franklin, Xiaojie Lu, Katie L. Bedard, LaShadric C. Grady, Jennifer D. Summerfield, Eric X. Shi, et al. "DNA-Encoded Library Hit Confirmation: Bridging the Gap Between On-DNA and Off-DNA Chemistry." ACS Medicinal Chemistry Letters 12, no. 7 (June 3, 2021): 1166–72. http://dx.doi.org/10.1021/acsmedchemlett.1c00156.

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27

Ji, Yue, Dongliang Dai, Huadong Luo, Simin Shen, Jing Fan, Zhao Wang, Min Chen, et al. "C–S Coupling of DNA-Conjugated Aryl Iodides for DNA-Encoded Chemical Library Synthesis." Bioconjugate Chemistry 32, no. 4 (March 15, 2021): 685–89. http://dx.doi.org/10.1021/acs.bioconjchem.1c00076.

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28

Reiher, Christopher A., David P. Schuman, Nicholas Simmons, and Scott E. Wolkenberg. "Trends in Hit-to-Lead Optimization Following DNA-Encoded Library Screens." ACS Medicinal Chemistry Letters 12, no. 3 (February 11, 2021): 343–50. http://dx.doi.org/10.1021/acsmedchemlett.0c00615.

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29

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 (February 28, 2021): 105–7. http://dx.doi.org/10.2533/chimia.2021.105.

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30

Krumb, Matthias, Lisa Marie Kammer, Shorouk O. Badir, María Jesús Cabrera-Afonso, Victoria E. Wu, Minxue Huang, Adam Csakai, Lisa A. Marcaurelle, and Gary A. Molander. "Photochemical C–H arylation of heteroarenes for DNA-encoded library synthesis." Chemical Science 13, no. 4 (2022): 1023–29. http://dx.doi.org/10.1039/d1sc05683b.

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DNA-encoded library technology has emerged as an efficient interrogation platform for the identification of therapeutic candidates in pharmaceutical settings. Herein, a direct photochemical C–H arylation of functionalized heteroarenes is reported.

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31

Park, Jun Hyung, Hee Myeong Wang, Min Hyeon Shin, and Hyun‐Suk Lim. "Synthesis of a DNA‐Encoded Library of Pyrrolo[2,3 ‐d ]pyrimidines." Bulletin of the Korean Chemical Society 42, no. 4 (February 8, 2021): 691–98. http://dx.doi.org/10.1002/bkcs.12243.

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32

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

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33

Ahn, Seungkirl, Alem W. Kahsai, Biswaranjan Pani, Qin-Ting Wang, Shuai Zhao, Alissa L. Wall, Ryan T. Strachan, et al. "Allosteric “beta-blocker” isolated from a DNA-encoded small molecule library." Proceedings of the National Academy of Sciences 114, no. 7 (January 27, 2017): 1708–13. http://dx.doi.org/10.1073/pnas.1620645114.

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The β2-adrenergic receptor (β2AR) has been a model system for understanding regulatory mechanisms of G-protein–coupled receptor (GPCR) actions and plays a significant role in cardiovascular and pulmonary diseases. Because all known β-adrenergic receptor drugs target the orthosteric binding site of the receptor, we set out to isolate allosteric ligands for this receptor by panning DNA-encoded small-molecule libraries comprising 190 million distinct compounds against purified human β2AR. Here, we report the discovery of a small-molecule negative allosteric modulator (antagonist), compound 15 [([4-((2S)-3-(((S)-3-(3-bromophenyl)-1-(methylamino)-1-oxopropan-2-yl)amino)-2-(2-cyclohexyl-2-phenylacetamido)-3-oxopropyl)benzamide], exhibiting a unique chemotype and low micromolar affinity for the β2AR. Binding of 15 to the receptor cooperatively enhances orthosteric inverse agonist binding while negatively modulating binding of orthosteric agonists. Studies with a specific antibody that binds to an intracellular region of the β2AR suggest that 15 binds in proximity to the G-protein binding site on the cytosolic surface of the β2AR. In cell-signaling studies, 15 inhibits cAMP production through the β2AR, but not that mediated by other Gs-coupled receptors. Compound 15 also similarly inhibits β-arrestin recruitment to the activated β2AR. This study presents an allosteric small-molecule ligand for the β2AR and introduces a broadly applicable method for screening DNA-encoded small-molecule libraries against purified GPCR targets. Importantly, such an approach could facilitate the discovery of GPCR drugs with tailored allosteric effects.

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34

MacConnell, Andrew B., Alexander K. Price, and Brian M. Paegel. "An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening." ACS Combinatorial Science 19, no. 3 (February 22, 2017): 181–92. http://dx.doi.org/10.1021/acscombsci.6b00192.

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35

Götte, Katharina, Silvia Chines, and Andreas Brunschweiger. "Reaction development for DNA-encoded library technology: From evolution to revolution?" Tetrahedron Letters 61, no. 22 (May 2020): 151889. http://dx.doi.org/10.1016/j.tetlet.2020.151889.

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36

Phelan, James P., Simon B. Lang, Jaehoon Sim, Simon Berritt, Andrew J. Peat, Katelyn Billings, Lijun Fan, and Gary A. Molander. "Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis." Journal of the American Chemical Society 141, no. 8 (February 12, 2019): 3723–32. http://dx.doi.org/10.1021/jacs.9b00669.

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37

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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38

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 (November 20, 2019): 9555–58. http://dx.doi.org/10.1021/acs.orglett.9b03726.

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39

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 (December 2020): 215–22. http://dx.doi.org/10.1016/j.bbrc.2020.04.033.

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40

Tian, Xia, Gregory S. Basarab, Nidhal Selmi, Thierry Kogej, Ying Zhang, Matthew Clark, and Robert A. Goodnow Jr. "Development and design of the tertiary amino effect reaction for DNA-encoded library synthesis." MedChemComm 7, no. 7 (2016): 1316–22. http://dx.doi.org/10.1039/c6md00088f.

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41

Arico-Muendel, Christopher C. "From haystack to needle: finding value with DNA encoded library technology at GSK." MedChemComm 7, no. 10 (2016): 1898–909. http://dx.doi.org/10.1039/c6md00341a.

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42

Lee, Kang Ju, Geul Bang, Yong Wook Kim, Min Hyeon Shin, and Hyun-Suk Lim. "Design and synthesis of a DNA-encoded combinatorial library of bicyclic peptoids." Bioorganic & Medicinal Chemistry 48 (October 2021): 116423. http://dx.doi.org/10.1016/j.bmc.2021.116423.

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43

Chen, Qiuxia, Xuemin Cheng, Lifang Zhang, Xianyang Li, Purui Chen, Jian Liu, Lanjun Zhang, Hong Wei, Zhonghan Li, and Dengfeng Dou. "Exploring the Lower Limit of Individual DNA-Encoded Library Molecules in Selection." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 5 (December 20, 2019): 523–29. http://dx.doi.org/10.1177/2472555219893949.

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DNA-encoded library (DEL) technology has been used as an ultra-high-throughput screening approach for hit identification of drug targets. This process is an affinity-based selection and requires incubation of DEL molecules with the target. Currently, in most reported cases, the input (i.e., the copy number) of individual DEL molecules varies from 105 to 107. With the ever-increasing DEL size and screening cost, lowering the input of DEL molecules while maintaining an appropriate signal-to-noise ratio in a selection is of paramount importance. In this article, we varied the input of DEL ranging from 103 to 105 in selections with two different protein targets to explore the lower limit of DEL molecule input. The results could facilitate the optimization of the DEL selection process and reduce costs related to library consumption.

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44

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 (June 18, 2007): 4755–58. http://dx.doi.org/10.1002/ange.200700654.

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45

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 (June 18, 2007): 4671–74. http://dx.doi.org/10.1002/anie.200700654.

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46

Wen, Xin, Xinyuan Wu, Rui Jin, and Xiaojie Lu. "Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization." European Journal of Medicinal Chemistry 248 (February 2023): 115079. http://dx.doi.org/10.1016/j.ejmech.2022.115079.

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47

Chan, Alix I., Lynn M. McGregor, Tara Jain, and David R. Liu. "Discovery of a Covalent Kinase Inhibitor from a DNA-Encoded Small-Molecule Library × Protein Library Selection." Journal of the American Chemical Society 139, no. 30 (July 20, 2017): 10192–95. http://dx.doi.org/10.1021/jacs.7b04880.

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48

Škopić, M. Klika, O. Bugain, K. Jung, S. Onstein, S. Brandherm, T. Kalliokoski, and A. Brunschweiger. "Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold." MedChemComm 7, no. 10 (2016): 1957–65. http://dx.doi.org/10.1039/c6md00243a.

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DNA-encoded libraries based on scaffolds functionalized for DNA-compatible chemistry were synthesized by split-and-pool combinatorial chemistry. The library design was aided by a chemoinformatic filtering cascade.

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49

Petersen, L. K., P. Blakskjær, A. Chaikuad, A. B. Christensen, J. Dietvorst, J. Holmkvist, S. Knapp, et al. "Novel p38α MAP kinase inhibitors identified from yoctoReactor DNA-encoded small molecule library." MedChemComm 7, no. 7 (2016): 1332–39. http://dx.doi.org/10.1039/c6md00241b.

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50

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 (April 25, 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 platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.

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