1
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Zhong S, Fang X, Wang Y, Zhang G, Li Y, Li Y. DNA-Compatible Diversification of Indole π-Activated Alcohols via a Direct Dehydrative Coupling Strategy. Org Lett 2022; 24:1022-1026. [PMID: 35050627 DOI: 10.1021/acs.orglett.1c04169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Indole-based diversification is highly desired in the DNA-encoded chemical library construction. Herein, we present a general strategy for on-DNA synthesis of diverse C3-functionalized indole derivatives via indole π-activated alcohol formation followed by direct dehydrative coupling. Highly efficient bond linkages of C-C, C-N, and C-S were achieved to fuse building blocks that are widely commercially available. DNA-encoding compatibility of the method has been further demonstrated to pave an avenue for application in constructing indole-focused three-dimensional libraries.
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Affiliation(s)
- Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
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2
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Du HC, Chen YC, Huang H. DNA-Compatible Nitro Reduction and Synthesis of Benzimidazoles. Methods Mol Biol 2022; 2541:67-73. [PMID: 36083546 DOI: 10.1007/978-1-0716-2545-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A key factor for productive DNA-encoded libraries is the chemical diversity of the small molecule moiety attached to an encoding DNA oligomer. The library structure diversity is often limited to DNA-compatible chemical reactions in aqueous media. Herein, we describe a facile process for reducing aryl nitro groups to aryl amines by using sodium dithionite (Na2S2O4). The new protocol offers simple operation and circumvents the pyrophoric potential of the conventional method (Raney nickel). The utility of this method is demonstrated by the versatile synthesis of benzimidazoles on DNA.
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Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Ying-Chu Chen
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Hongbing Huang
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA.
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3
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Gao Y, Sun Y, Fang X, Zhao G, Li X, Zhang G, Li Y, Li Y. Development of on-DNA vinyl sulfone synthesis for DNA-encoded chemical libraries. Org Chem Front 2022. [DOI: 10.1039/d2qo00881e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present the development of an efficient synthetic route to generate a DNA-compatible vinyl sulfone functional group, and the subsequent chemical transformations demonstrated the feasibility of our method in DEL construction.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xufeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China
- Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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4
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Fair RJ, Walsh RT, Hupp CD. The expanding reaction toolkit for DNA-encoded libraries. Bioorg Med Chem Lett 2021; 51:128339. [PMID: 34478840 DOI: 10.1016/j.bmcl.2021.128339] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022]
Abstract
Over the past decade, DNA-encoded libraries (DELs) have emerged as a leading platform for small molecule drug discovery among pharmaceutical companies, biotech companies and academic drug hunters alike. This revolutionary technology has tremendous potential that is yet to be fully realized, as the exploration of therapeutically relevant chemical space is fueled by the ever-expanding repertoire of DNA-compatible reactions used to construct the libraries. Advances in direct coupling reactions, like photo-catalytic cross couplings, unique cyclizations such as the formation of 1,2,4-oxadiazoles, and new functional group transformations are valuable contributions to the DEL reaction toolkit, and indicate where future reaction development efforts should focus in order to maximize the productivity of DELs.
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Affiliation(s)
| | - Ryan T Walsh
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
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5
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Götte K, Chines S, Brunschweiger A. Reaction development for DNA-encoded library technology: From evolution to revolution? Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151889] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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6
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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7
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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8
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Geigle SN, Petersen AC, Satz AL. Development of DNA-Compatible Van Leusen Three-Component Imidazole Synthesis. Org Lett 2019; 21:9001-9004. [DOI: 10.1021/acs.orglett.9b03406] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Kunig VBK, Ehrt C, Dömling A, Brunschweiger A. Isocyanide Multicomponent Reactions on Solid-Phase-Coupled DNA Oligonucleotides for Encoded Library Synthesis. Org Lett 2019; 21:7238-7243. [PMID: 31464126 DOI: 10.1021/acs.orglett.9b02448] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isocyanide multicomponent reactions play a prominent role in drug discovery. This chemistry has hardly been investigated for compatibility with DNA-encoded combinatorial synthesis. The Ugi, Ugi-azide, and Groebke-Blackburn-Bienaymé reactions are well-tolerated by DNA on the solid phase and show a broad scope. However, an oxadiazole-forming variant of the Ugi reaction caused DNA depurination, requiring a more stable hexathymidine DNA for encoded library synthesis. Cheminformatic analysis revealed that isocyanide multicomponent-reaction-based encoded libraries cover a diverse chemical space.
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Affiliation(s)
- Verena B K Kunig
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Alexander Dömling
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
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10
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Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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11
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
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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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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12
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Phelan JP, Lang SB, Sim J, Berritt S, Peat AJ, Billings K, Fan L, Molander GA. Open-Air Alkylation Reactions in Photoredox-Catalyzed DNA-Encoded Library Synthesis. J Am Chem Soc 2019; 141:3723-3732. [PMID: 30753065 DOI: 10.1021/jacs.9b00669] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA-encoded library (DEL) technology is a powerful tool commonly used by the pharmaceutical industry for the identification of compounds with affinity to biomolecular targets. Success in this endeavor lies in sampling diverse chemical libraries. However, current DELs tend to be deficient in C(sp3) carbon counts. We report unique solutions to the challenge of increasing both the chemical diversity of these libraries and their C(sp3) carbon counts by merging Ni/photoredox dual catalytic C(sp2)-C(sp3) cross-coupling as well as photoredox-catalyzed radical/polar crossover alkylation protocols with DELs. The successful integration of multiple classes of radical sources enables the rapid incorporation of a diverse set of alkyl fragments.
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Affiliation(s)
- James P Phelan
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon B Lang
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Simon Berritt
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Andrew J Peat
- GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Katelyn Billings
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Lijun Fan
- GlaxoSmithKline , 200 Cambridge Park Drive , Cambridge , Massachusetts 02140 , United States
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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13
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de Pedro Beato E, Priego J, Gironda-Martínez A, González F, Benavides J, Blas J, Martín-Ortega MD, Toledo MÁ, Ezquerra J, Torrado A. Mild and Efficient Palladium-Mediated C-N Cross-Coupling Reaction between DNA-Conjugated Aryl Bromides and Aromatic Amines. ACS COMBINATORIAL SCIENCE 2019; 21:69-74. [PMID: 30615417 DOI: 10.1021/acscombsci.8b00142] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA-encoded library technology (ELT) has emerged in the pharmaceutical industry as a powerful tool for hit and lead generation. Over the last 10 years, a number of DNA-compatible chemical reactions have been published and used to synthesize libraries. Among the most commonly used reactions in medicinal chemistry is the C-N bond formation, and its application to DNA-encoded library technology affords an alternative approach to identify high-affinity binders for biologically relevant protein targets. Herein we report a newly developed Pd-promoted C-N cross coupling reaction between DNA-conjugated aryl bromides and a wide scope of arylamines in good to excellent yields. The mild reaction conditions should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
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Affiliation(s)
| | - Julián Priego
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | - Fernando González
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Benavides
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Blas
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | | | - Jesús Ezquerra
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Alicia Torrado
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
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14
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Li H, Sun Z, Wu W, Wang X, Zhang M, Lu X, Zhong W, Dai D. Inverse-Electron-Demand Diels-Alder Reactions for the Synthesis of Pyridazines on DNA. Org Lett 2018; 20:7186-7191. [PMID: 30365326 DOI: 10.1021/acs.orglett.8b03114] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The synthesis of pyridazines on DNA has been developed on the basis of inverse-electron-demand Diels-Alder (IEDDA) reactions of 1,2,4,5-tetrazines. The broad substrate scope is explored. Functionalized pyridazine products are selected for subsequent DNA-compatible Suzuki-Miyaura coupling, acylation, and SNAr substitution reactions, demonstrating the feasibility and versatility of IEDDA reactions for DNA-encoded library synthesis.
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Affiliation(s)
- Hailong Li
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Zhen Sun
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Wenting Wu
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Xuan Wang
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Science , 501 Haike Road, Zhang Jiang Hi-Tech Park , Pudong, Shanghai 201203 , P. R. China
| | - Mingqiang Zhang
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica , Chinese Academy of Science , 501 Haike Road, Zhang Jiang Hi-Tech Park , Pudong, Shanghai 201203 , P. R. China
| | - Wenge Zhong
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
| | - Dongcheng Dai
- Department of Discovery Modalities , Amgen Asia R&D Center, Amgen Research , 4560 Jinke Road , Pudong, Shanghai 201210 , P. R. China
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15
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Pels K, Dickson P, An H, Kodadek T. DNA-Compatible Solid-Phase Combinatorial Synthesis of β-Cyanoacrylamides and Related Electrophiles. ACS COMBINATORIAL SCIENCE 2018; 20:61-69. [PMID: 29298042 DOI: 10.1021/acscombsci.7b00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We demonstrate that the Knoevenagel condensation can be exploited in combinatorial synthesis on the solid phase. Condensation products from such reactions were structurally characterized, and their Michael reactivity with thiol and phosphine nucleophiles is described. Cyanoacrylamides were previously reported to react reversibly with thiols, and notably, we show that dilution into low pH buffer can trap covalent adducts, which are isolable via chromatography. Finally, we synthesized both traditional and DNA-encoded one-bead, one-compound libraries containing cyanoacrylamides as a source of cysteine-reactive reversibly covalent protein ligands.
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Affiliation(s)
- Kevin Pels
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Paige Dickson
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hongchan An
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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16
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Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery,
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hongbing Huang
- Center for Drug Discovery,
Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
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17
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Škopić MK, Salamon H, Bugain O, Jung K, Gohla A, Doetsch LJ, Dos Santos D, Bhat A, Wagner B, Brunschweiger A. Acid- and Au(i)-mediated synthesis of hexathymidine-DNA-heterocycle chimeras, an efficient entry to DNA-encoded libraries inspired by drug structures. Chem Sci 2017; 8:3356-3361. [PMID: 28507705 PMCID: PMC5416911 DOI: 10.1039/c7sc00455a] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/27/2017] [Indexed: 11/21/2022] Open
Abstract
Libraries of DNA-tagged compounds are a validated screening technology for drug discovery. They are synthesized through combinatorial iterations of alternated coding and preparative synthesis steps. Thus, large chemical space can be accessed for target-based screening. However, the need to preserve the functionality of the DNA tag severely restricts the choice of chemical methods for library synthesis. Acidic organocatalysts, transition metals, and oxidants furnish diverse drug-like structures from simple starting materials, but cause loss of genetic information by depurination. A hexathymidine oligonucleotide, called "hexT" allows the chemist utilizing these classes of catalysts to access a potentially broad variety of structures in the initial step of library synthesis. We exploited its catalyst tolerance to efficiently synthesize diverse substituted β-carbolines, pyrazolines, and pyrazoles from readily available starting materials as hexT conjugates by acid- and Au(i)-catalysis, respectively. The hexT conjugates were ligated to coding DNA sequences yielding encoded screening libraries inspired by drug structures.
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Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Hazem Salamon
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Olivia Bugain
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Kathrin Jung
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Anne Gohla
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Lara J Doetsch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Denise Dos Santos
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Avinash Bhat
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Bernd Wagner
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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18
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Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
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19
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Fan L, Davie CP. Zirconium(IV)-Catalyzed Ring Opening of on-DNA Epoxides in Water. Chembiochem 2017; 18:843-847. [DOI: 10.1002/cbic.201600563] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Lijun Fan
- GlaxoSmithKline; Platform Technology & Science; 830 Winter Street Waltham MA 02451 USA
| | - Christopher P. Davie
- GlaxoSmithKline; Platform Technology & Science; 830 Winter Street Waltham MA 02451 USA
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20
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Klika Škopić M, Willems S, Wagner B, Schieven J, Krause N, Brunschweiger A. Exploration of a Au(i)-mediated three-component reaction for the synthesis of DNA-tagged highly substituted spiroheterocycles. Org Biomol Chem 2017; 15:8648-8654. [DOI: 10.1039/c7ob02347b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A gold(i)-mediated reaction to a DNA-tagged spirocycle, and the tolerance of different nucleic acids to the reaction conditions are demonstrated.
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Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Suzanne Willems
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Bernd Wagner
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Justin Schieven
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Norbert Krause
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
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21
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Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
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22
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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23
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Škopić MK, Bugain O, Jung K, Onstein S, Brandherm S, Kalliokoski T, Brunschweiger A. Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00243a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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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Affiliation(s)
- M. Klika Škopić
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - O. Bugain
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - K. Jung
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Onstein
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Brandherm
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | | | - A. Brunschweiger
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
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