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Yi Y, An HW, Wang H. Intelligent Biomaterialomics: Molecular Design, Manufacturing, and Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2305099. [PMID: 37490938 DOI: 10.1002/adma.202305099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Materialomics integrates experiment, theory, and computation in a high-throughput manner, and has changed the paradigm for the research and development of new functional materials. Recently, with the rapid development of high-throughput characterization and machine-learning technologies, the establishment of biomaterialomics that tackles complex physiological behaviors has become accessible. Breakthroughs in the clinical translation of nanoparticle-based therapeutics and vaccines have been observed. Herein, recent advances in biomaterials, including polymers, lipid-like materials, and peptides/proteins, discovered through high-throughput screening or machine learning-assisted methods, are summarized. The molecular design of structure-diversified libraries; high-throughput characterization, screening, and preparation; and, their applications in drug delivery and clinical translation are discussed in detail. Furthermore, the prospects and main challenges in future biomaterialomics and high-throughput screening development are highlighted.
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Affiliation(s)
- Yu Yi
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hong-Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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2
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Ramiro JL, Martínez-Caballero S, Neo AG, Díaz J, Marcos CF. The Castagnoli–Cushman Reaction. Molecules 2023; 28:molecules28062654. [PMID: 36985626 PMCID: PMC10058692 DOI: 10.3390/molecules28062654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Since the first reports of the reaction of imines and cyclic anhydrides by Castagnoli and Cushman, this procedure has been applied to the synthesis of a variety of lactams, some of them with important synthetic or biological interest. The scope of the reaction has been extended to the use of various Schiff bases and anhydrides as well as to different types of precursors for these reagents. In recent years, important advances have been made in understanding the mechanism of the reaction, which has historically been quite controversial. This has helped to develop reaction conditions that lead to pure diastereomers and even homochiral products. In addition, these mechanistic studies have also led to the development of new multicomponent versions of the Castagnoli–Cushman reaction that allow products with more diverse and complex molecular structures to be easily obtained.
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Affiliation(s)
- José Luis Ramiro
- Laboratory of Bioorganic Chemistry & Membrane Biophysics (L.O.B.O.), Departamento de Química Orgánica e Inorgánica, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Sonia Martínez-Caballero
- Departamento de Didáctica de las Ciencias Experimentales y las Matemáticas, Facultad de Formación de Profesorado, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Ana G. Neo
- Laboratory of Bioorganic Chemistry & Membrane Biophysics (L.O.B.O.), Departamento de Química Orgánica e Inorgánica, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
- Correspondence: (A.G.N.); (C.F.M.)
| | - Jesús Díaz
- Laboratory of Bioorganic Chemistry & Membrane Biophysics (L.O.B.O.), Departamento de Química Orgánica e Inorgánica, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Carlos F. Marcos
- Laboratory of Bioorganic Chemistry & Membrane Biophysics (L.O.B.O.), Departamento de Química Orgánica e Inorgánica, Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
- Correspondence: (A.G.N.); (C.F.M.)
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3
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Wen X, Wu X, Jin R, Lu X. Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization. Eur J Med Chem 2023; 248:115079. [PMID: 36669370 DOI: 10.1016/j.ejmech.2022.115079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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4
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Chines S, Ehrt C, Potowski M, Biesenkamp F, Grützbach L, Brunner S, van den Broek F, Bali S, Ickstadt K, Brunschweiger A. Navigating chemical reaction space - application to DNA-encoded chemistry. Chem Sci 2022; 13:11221-11231. [PMID: 36320474 PMCID: PMC9517168 DOI: 10.1039/d2sc02474h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Databases contain millions of reactions for compound synthesis, rendering selection of reactions for forward synthetic design of small molecule screening libraries, such as DNA-encoded libraries (DELs), a big data challenge. To support reaction space navigation, we developed the computational workflow Reaction Navigator. Reaction files from a large chemistry database were processed using the open-source KNIME Analytics Platform. Initial processing steps included a customizable filtering cascade that removed reactions with a high probability to be incompatible with DEL, as they would e.g. damage the genetic barcode, to arrive at a comprehensive list of transformations for DEL design with applicability potential. These reactions were displayed and clustered by user-defined molecular reaction descriptors which are independent of reaction core substitution patterns. Thanks to clustering, these can be searched manually to identify reactions for DEL synthesis according to desired reaction criteria, such as ring formation or sp3 content. The workflow was initially applied for mapping chemical reaction space for aromatic aldehydes as an exemplary functional group often used in DEL synthesis. Exemplary reactions have been successfully translated to DNA-tagged substrates and can be applied to library synthesis. The versatility of the Reaction Navigator was then shown by mapping reaction space for different reaction conditions, for amines as a second set of starting materials, and for data from a second database.
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Affiliation(s)
- Silvia Chines
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | | | - Marco Potowski
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Felix Biesenkamp
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Lars Grützbach
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
| | - Susanne Brunner
- TU Dortmund University, Department of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | | | - Shilpa Bali
- Elsevier B.V. Radarweg 29 1043 NX Amsterdam The Netherlands
| | - Katja Ickstadt
- TU Dortmund University, Department of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Department of Chemistry and Chemical Biology Otto-Hahn-Str. 6 44227 Dortmund Germany
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5
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Hunter JH, Potowski M, Stanway-Gordon HA, Madin A, Pairaudeau G, Brunschweiger A, Waring MJ. Functional Group Tolerance of a Micellar on-DNA Suzuki-Miyaura Cross-Coupling Reaction for DNA-Encoded Library Design. J Org Chem 2021; 86:17930-17935. [PMID: 34816720 DOI: 10.1021/acs.joc.1c02259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA-encoded libraries (DELs) offer great promise for the discovery of new ligands for proteins. Many current reactions used for DEL synthesis do not proceed efficiently over a wide range of substrates. Combining a diverse array of multicomponent reactions with micellar-promoted Suzuki-Miyaura cross-coupling provides a strategy for synthesizing highly diverse DELs with exceptionally high fidelity. These results demonstrate that the micellar Suzuki-Miyaura reaction has exceptional functional group tolerance and broad applicability.
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Affiliation(s)
- James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Marco Potowski
- Research Group Medicinal Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Garry Pairaudeau
- Exscientia, Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Andreas Brunschweiger
- Research Group Medicinal Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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6
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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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7
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemisch stabilisierte DNA‐Codes für DNA‐kodierte Chemie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Potowski
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Verena B. K. Kunig
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Lukas Eberlein
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Stefan M. Kast
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Andreas Brunschweiger
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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8
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry. Angew Chem Int Ed Engl 2021; 60:19744-19749. [PMID: 34153170 PMCID: PMC8456907 DOI: 10.1002/anie.202104348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Indexed: 12/18/2022]
Abstract
DNA‐encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7‐deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson–Crick pairs, yielded ligation‐competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid‐ and metal ion‐promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid‐promoted Pictet–Spengler and Biginelli reactions, and metal‐promoted pyrazole syntheses on controlled pore glass‐coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification.
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Affiliation(s)
- Marco Potowski
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Verena B K Kunig
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lukas Eberlein
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | | | - Stefan M Kast
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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9
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Potowski M, Lüttig R, Vakalopoulos A, Brunschweiger A. Copper(I/II)-Promoted Diverse Imidazo[1,2-α]pyridine Synthesis on Solid-Phase Bound DNA Oligonucleotides for Encoded Library Design. Org Lett 2021; 23:5480-5484. [PMID: 34181416 DOI: 10.1021/acs.orglett.1c01834] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-encoded libraries designed around heterocyclic scaffolds have proven highly productive in target-based screening. Here, we show the synthesis of imidazopyridines on a controlled pore glass-coupled DNA oligonucleotide for solid phase-initiated encoded library synthesis. The target compounds were synthesized by a variant of the A3 coupling reaction from aminopyridines, alkynes, and aldehydes promoted by copper(I/II) and furnished diverse substituted scaffolds with functionalities for library design. Although proceeding under forcing conditions, it produced minimal DNA damage.
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Affiliation(s)
- Marco Potowski
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Ricarda Lüttig
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | | | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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10
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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11
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Kölmel DK, Zhu H, Flanagan ME, Sakata SK, Harris AR, Wan J, Morgan BA. Employing Photocatalysis for the Design and Preparation of DNA‐Encoded Libraries: A Case Study. CHEM REC 2021; 21:616-630. [DOI: 10.1002/tcr.202000148] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Dominik K. Kölmel
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Hongyao Zhu
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Mark E. Flanagan
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Sylvie K. Sakata
- Worldwide Research and Development Pfizer Inc 10770 Science Center Drive San Diego CA 92121 United States
| | - Anthony R. Harris
- Worldwide Research and Development Pfizer Inc Eastern Point Road Groton CT 06340 United States
| | - Jinqiao Wan
- HitGen Inc Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District Chengdu City Sichuan Province P. R. China
| | - Barry A. Morgan
- HitGen Inc Building 6, No. 8 Huigu first East Road, Tianfu International Bio-Town, Shuangliu District Chengdu City Sichuan Province P. R. China
- HitGen Pharmaceuticals Inc PO Box 88240 Houston TX 77288 United States
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12
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On-resin multicomponent protocols for biopolymer assembly and derivatization. Nat Protoc 2021; 16:561-578. [PMID: 33473197 DOI: 10.1038/s41596-020-00445-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/13/2020] [Indexed: 01/29/2023]
Abstract
Solid-phase synthesis represents the methodological showcase for technological advances such as split-and-pool combinatorial chemistry and the automated synthesis of peptides, nucleic acids and polysaccharides. These strategies involve iterative coupling cycles that do not generate functional diversity besides that incorporated by the amino acids, nucleosides and monosaccharide building blocks. In sharp contrast, multicomponent reactions (MCRs) are traditionally used to generate both skeletal and appendage diversity in short, batchwise procedures. On-resin MCRs have traditionally been employed for the construction of heterocycle and peptidomimetic libraries, but that scenario has changed recently, and today the focus is more on the solid-phase derivatization of peptides and oligonucleotides. This review presents relevant experimental details and addresses the synthetic scope of such on-resin multicomponent protocols employed to accomplish specific biopolymer covalent modifications that are practically inviable by traditional solution-phase methodologies. Recommendations are provided to facilitate the implementation of solid-supported protocols and avoid possible pitfalls associated with the selection of the polymeric resin, the solvent and the order and amount of the reagents employed. We describe procedures comprising the multicomponent lipidation, biotinylation and labeling of both termini and the side chains, as well as the use of MCRs in the traceless on-resin synthesis of ligated and cyclic peptides. Solid-phase protocols for the assembly of α-helical and parallel β-sheet peptides as well as hybrid peptide-peptoid and peptide-peptide nucleic acid architectures are described. Finally, the solid-supported multicomponent derivatization of DNA oligonucleotides is illustrated as part of the DNA-encoded library technology relying on MCR-derived heterocyclic compounds.
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13
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Liu S, Qi J, Lu W, Wang X, Lu X. Synthetic Studies toward DNA-Encoded Heterocycles Based on the On-DNA Formation of α,β-Unsaturated Ketones. Org Lett 2021; 23:908-913. [PMID: 33444029 DOI: 10.1021/acs.orglett.0c04118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Taking advantage of the diversity-oriented synthesis strategy with α,β-unsaturated carbonyl compounds, we have successfully established the DNA-compatible transformations for various heterocyclic scaffolds. The ring-closure reactions for pyrrole, pyrrolidine, pyrazole, pyrazoline, isoxazoline, pyridine, piperidine, cyclohexenone, and 5,8-dihydroimidazo[1,2-a]pyrimidine were elegantly demonstrated in a DNA-compatible format. These efforts paved the way for preparing DNA-encoded libraries with more extensive chemical space.
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Affiliation(s)
- Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingjing Qi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
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14
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Kölmel DK, Ratnayake AS, Flanagan ME. Photoredox cross-electrophile coupling in DNA-encoded chemistry. Biochem Biophys Res Commun 2020; 533:201-208. [DOI: 10.1016/j.bbrc.2020.04.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/06/2020] [Indexed: 12/22/2022]
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15
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Yuen J, Chai J, Ding Y. Condensation of DNA-Conjugated Imines with Homophthalic Anhydride for the Synthesis of Isoquinolones on DNA. Bioconjug Chem 2020; 31:2712-2718. [DOI: 10.1021/acs.bioconjchem.0c00508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Josephine Yuen
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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16
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Price AK, Paegel BM. Considerations for Achieving Maximized DNA Recovery in Solid-Phase DNA-Encoded Library Synthesis. ACS COMBINATORIAL SCIENCE 2020; 22:649-655. [PMID: 32786319 DOI: 10.1021/acscombsci.0c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded library (DEL) technology enables rapid, economical synthesis, and exploration of novel chemical space. Reaction development for DEL synthesis has recently accelerated in pace with a specific emphasis on ensuring that the reaction does not compromise the integrity of the encoding DNA. However, the factors that contribute to a reaction's "DNA compatibility" remain relatively unknown. We investigated several solid-phase reactions and encoding conditions and determined their impact on DNA compatibility. Conditions that minimized the accessibility of reactive groups on the DNA encoding tag (switching solvent, low temperature, double-stranded encoding tag) significantly improved compatibility. We showcased this approach in the multistep synthesis of an acyldepsipeptide (ADEP1) fragment, which preserved 73% of DNA for a >100-fold improvement over canonical conditions. These results are particularly encouraging in the context of multistep reaction sequences to access natural product-like scaffolds and more broadly underscore the importance of reconciling the biophysical properties and reactivity of DNA with chemistry development to yield high-quality libraries of those scaffolds.
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Affiliation(s)
- Alexander K. Price
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry Scripps Research 130 Scripps Way, Jupiter, Florida 33458, United States
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17
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Adamovskyi M, Avramenko MM, Volochnyuk DM, Ryabukhin SV. Fluoral Hydrate: A Perspective Substrate for the Castagnoli-Cushman Reaction. ACS OMEGA 2020; 5:20932-20942. [PMID: 32875228 PMCID: PMC7450650 DOI: 10.1021/acsomega.0c02394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
The reactivity of azomethines based on trifluoroacetaldehyde hydrate in the Castagnoli-Cushman reaction (CCR) was researched. The impact of the nature of anhydrides explored on the reaction route was determined. The preparative procedures for the synthesis of N-substituted (3R*,4R*)-1-oxo-3-(trifluoromethyl)-1,2,3,4-tetrahydroisoquinoline-4-carboxylic and (1R*,2R*)-4-oxo-2-(trifluoromethyl)-2,3,4,5-tetrahydro-1H-benzo[d]azepine-1-carboxylic acids in gram scales were elaborated. It was shown that the trifluoromethyl group remarkably decreased the reactivity of azomethines in CCR. The mechanism for the formation of different products depending on the anhydride's nature was proposed.
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Affiliation(s)
- Mykhailo
I. Adamovskyi
- Enamine
Ltd., Chervonotkatska
Street 78, Kyiv 02094, Ukraine
- Taras
Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01601, Ukraine
| | - Mykola M. Avramenko
- Enamine
Ltd., Chervonotkatska
Street 78, Kyiv 02094, Ukraine
- Taras
Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01601, Ukraine
| | - Dmitriy M. Volochnyuk
- Enamine
Ltd., Chervonotkatska
Street 78, Kyiv 02094, Ukraine
- Taras
Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01601, Ukraine
- Institute
of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine
| | - Sergey V. Ryabukhin
- Enamine
Ltd., Chervonotkatska
Street 78, Kyiv 02094, Ukraine
- Taras
Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01601, Ukraine
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18
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
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19
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020; 59:14965-14972. [PMID: 32436364 DOI: 10.1002/anie.202005070] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Indexed: 11/11/2022]
Abstract
Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.
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Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China.,Department of Chemistry, Southern University of Science and Technology China, 1088 Xueyuan Road, Shenzhen, China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
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20
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Firsov A, Bakulina O, Dar'in D, Guranova N, Krasavin M. Further Insight into the Castagnoli-Cushman-type Synthesis of 1,4,6-Trisubstituted 1,6-Dihydropyridin-2-(3 H)-ones from 3-Arylglutaconic Acid Anhydrides. J Org Chem 2020; 85:6822-6829. [PMID: 32338899 DOI: 10.1021/acs.joc.0c00836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The earlier reported three-component Castagnoli-Cushman-type synthesis of 1,4,6-trisubstituted 1,6-dihydropyridin-2-(3H)-ones from 3-arylglutaconic acids, primary amines, and aromatic aldehydes has been further investigated. It was shown to proceed via 3-arylglutaconic anhydrides, which, in turn, were found to give superior results in the two-component reactions with imines. The initial formation of the Castagnoli-Cushman carboxylic acids was shown to be the case, and their decarboxylation was found to follow a complex, "forked" pathway, which was confirmed by deuterium incorporation experiments.
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Affiliation(s)
- Andrei Firsov
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Olga Bakulina
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Dmitry Dar'in
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Natalia Guranova
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
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21
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Li J, Li Y, Lu F, Liu L, Ji Q, Song K, Yin Q, Lerner RA, Yang G, Xu H, Ma P. A DNA-encoded library for the identification of natural product binders that modulate poly (ADP-ribose) polymerase 1, a validated anti-cancer target. Biochem Biophys Res Commun 2020; 533:241-248. [PMID: 32381359 DOI: 10.1016/j.bbrc.2020.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 01/01/2023]
Abstract
Natural products have been an invaluable source of drug discovery, but their targets remain largely unknown. Natural products enriched DNA-encoded chemical libraries (nDELs) empower the researchers to rapidly and economically screen numerous natural products against various protein targets, and therefore promote the elucidation of the molecular mechanisms. In this work, we used poly (ADP-ribose) polymerase 1 (PARP1), as an example to explore the usage of nDEL for the functional natural products selection. We used late-stage modification approach to label three positive binders with unique DNA barcodes, whose dissociation constants range from sub-micromolar to micromolar. The selection criterion was set up according to the enrichment of these controls. Five natural products selected by this criterion directly bind to PARP1 in SPR, among which luteolin exhibits the highest inhibitory activity against PARP1. Moreover, luteolin selectively induces accumulation of DNA double-strand breaks and G2/M phase arrest in BRCA-deficient cells. All the findings from these investigations on luteolin support that PARP1 inhibition is one of the mechanisms for its anti-cancer activity.
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Affiliation(s)
- Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, China; University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Ke Song
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Qianqian Yin
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
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22
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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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23
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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: 46] [Impact Index Per Article: 11.5] [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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24
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Westphal MV, Hudson L, Mason JW, Pradeilles JA, Zécri FJ, Briner K, Schreiber SL. Water-Compatible Cycloadditions of Oligonucleotide-Conjugated Strained Allenes for DNA-Encoded Library Synthesis. J Am Chem Soc 2020; 142:7776-7782. [PMID: 32267148 DOI: 10.1021/jacs.9b13186] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-encoded libraries of small molecules are being explored extensively for the identification of binders in early drug-discovery efforts. Combinatorial syntheses of such libraries require water- and DNA-compatible reactions, and the paucity of these reactions currently limit the chemical features of resulting barcoded products. The present work introduces strain-promoted cycloadditions of cyclic allenes under mild conditions to DNA-encoded library synthesis. Owing to distinct cycloaddition modes of these reactive intermediates with activated olefins, 1,3-dipoles, and dienes, the process generates diverse molecular architectures from a single precursor. The resulting DNA-barcoded compounds exhibit unprecedented ring and topographic features, related to elements found to be powerful in phenotypic screening.
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Affiliation(s)
- Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Johan A Pradeilles
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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25
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Kölmel DK, Ratnayake AS, Flanagan ME, Tsai MH, Duan C, Song C. Photocatalytic [2 + 2] Cycloaddition in DNA-Encoded Chemistry. Org Lett 2020; 22:2908-2913. [PMID: 32239950 DOI: 10.1021/acs.orglett.0c00574] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The on-DNA synthesis of highly substituted cyclobutanes was achieved through a photocatalytic [2 + 2] cycloaddition reaction in aqueous solution. Readily available DNA-tagged styrene derivatives were reacted with structurally diverse cinnamates in the presence of an iridium-based photocatalyst, Ir(ppy)2(dtbbpy)PF6, to forge two new C(sp3)-C(sp3) bonds. This transformation was demonstrated to have excellent functional group tolerance and allowed for the facile installation of a variety of heteroaromatic substituents on a densely functionalized cyclobutane scaffold.
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Affiliation(s)
- Dominik K Kölmel
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mei-Hsuan Tsai
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Cong Duan
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Chao Song
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
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26
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Potowski M, Esken R, Brunschweiger A. Translation of the copper/bipyridine-promoted Petasis reaction to solid phase-coupled DNA for encoded library synthesis. Bioorg Med Chem 2020; 28:115441. [PMID: 32222338 DOI: 10.1016/j.bmc.2020.115441] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/28/2020] [Accepted: 03/12/2020] [Indexed: 11/28/2022]
Abstract
The Petasis three-component reaction gives rise to diverse substituted α-aryl glycines from readily available amines, boronic acids and glyoxalic acid. Thus, this reaction is highly attractive for DNA-encoded small molecule screening library synthesis. The Petasis reaction is for instance promoted by a potentially DNA damaging copper(I)/bipyridine reagent system in dry organic solvents. We found that solid phase-coupled DNA strands tolerated this reagent system at elevated temperature allowing for synthesis of diverse substituted DNA-tagged α-aryl glycines from DNA-conjugated secondary amines.
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Affiliation(s)
- Marco Potowski
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Robin Esken
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany.
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27
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Potowski M, Losch F, Wünnemann E, Dahmen JK, Chines S, Brunschweiger A. Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions. Chem Sci 2019; 10:10481-10492. [PMID: 32055372 PMCID: PMC7003951 DOI: 10.1039/c9sc04708e] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022] Open
Abstract
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.
DNA-encoded compound libraries are a widely used technology for target-based small molecule screening. Generally, these libraries are synthesized by solution phase combinatorial chemistry requiring aqueous solvent mixtures and reactions that are orthogonal to DNA reactivity. Initiating library synthesis with readily available controlled pore glass-coupled DNA barcodes benefits from enhanced DNA stability due to nucleobase protection and choice of dry organic solvents for encoded compound synthesis. We screened the compatibility of solid-phase coupled DNA sequences with 53 metal salts and organic reagents. This screening experiment suggests design of encoded library synthesis. Here, we show the reaction optimization and scope of three sp3-bond containing heterocyclic scaffolds synthesized on controlled pore glass-connected DNA sequences. A ZnCl2-promoted aza-Diels–Alder reaction with Danishefsky's diene furnished diverse substituted DNA-tagged pyridones, and a phosphoric acid organocatalyst allowed for synthesis of tetrahydroquinolines by the Povarov reaction and pyrimidinones by the Biginelli reaction, respectively. These three reactions caused low levels of DNA depurination and cover broad and only partially overlapping chemical space though using one set of DNA-coupled starting materials.
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Affiliation(s)
- Marco Potowski
- 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 .
| | - Elena Wünnemann
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Janina K Dahmen
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Silvia Chines
- 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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28
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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: 51] [Impact Index Per Article: 10.2] [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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29
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Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
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