1
|
Siripuram V, Sunkari YK, Ma F, Nguyen TL, Flajolet M. Reversible and Fully Controllable Generation of Organo-Soluble DNA (osDNA). ACS OMEGA 2024; 9:14771-14780. [PMID: 38585059 PMCID: PMC10993399 DOI: 10.1021/acsomega.3c06755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 04/09/2024]
Abstract
The present work describes a complete and reversible transformation of DNA's properties allowing solubilization in organic solvents and subsequent chemical modifications that are otherwise not possible in an aqueous medium. Organo-soluble DNA (osDNA) moieties are generated by covalently linking a dsDNA fragment to a polyether moiety with a built-in mechanism, rendering the process perfectly reversible and fully controllable. The precise removal of the polyether moiety frees up the initial DNA fragment, unaltered, both in sequence and nature. The solubility of osDNA was confirmed in six organic solvents of decreasing polarity and six types of osDNAs. As a proof of concept, in the context of DNA-encoded library (DEL) technology, an amidation reaction was successfully performed on osDNA in 100% DMSO. The development of osDNA opens up entirely new avenues for any DNA applications that could benefit from working in nonaqueous solutions, including chemical transformations.
Collapse
Affiliation(s)
- Vijay
Kumar Siripuram
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Yashoda Krishna Sunkari
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Fei Ma
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Thu-Lan Nguyen
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| | - Marc Flajolet
- Laboratory of Molecular and
Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York City, New York 10065, United States
| |
Collapse
|
2
|
Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
Collapse
Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
3
|
Sunkari YK, Nguyen TL, Siripuram VK, Flajolet M. Impact of organic chemistry conditions on DNA durability in the context of DNA-encoded library technology. iScience 2023; 26:107573. [PMID: 37664608 PMCID: PMC10470182 DOI: 10.1016/j.isci.2023.107573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2023] [Accepted: 08/05/2023] [Indexed: 09/05/2023] Open
Abstract
High-power screening (HPS) technologies, such as DNA-encoded library (DEL) technology, could exponentially increase the dimensions of the chemical space accessible for drug discovery. The intrinsic fragile nature of DNA is associated with cumbersome limitations and DNA durability (e.g., depurination, loss of phosphate groups, adduct formation) is compromised in numerous organic chemistry conditions that require empirical testing. An atlas of reaction conditions (temperature, pH, solvent/buffer, ligands, oxidizing reagents, catalysts, scavengers in function of time) that have been systematically tested in multiple combinations, indicates precisely limits useful for DEL construction. More importantly, this approach could be used broadly to effectively evaluate DNA-compatibility of any novel on-DNA chemical reaction, and it is compatible with different molecular methodologies. This atlas and the general approach presented, by allowing novel reaction conditions to be performed in presence of DNA, should greatly help in expanding the DEL chemical space as well as any field involving DNA durability.
Collapse
Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| |
Collapse
|
4
|
Zhan F, Zhu J, Xie S, Xu J, Xu S. Advances of bioorthogonal coupling reactions in drug development. Eur J Med Chem 2023; 253:115338. [PMID: 37037138 DOI: 10.1016/j.ejmech.2023.115338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Currently, bioorthogonal coupling reactions have garnered considerable interest due to their high substrate selectivity and less restrictive reaction conditions. During recent decades, bioorthogonal coupling reactions have emerged as powerful tools in drug development. This review describes the current applications of bioorthogonal coupling reactions in compound library building mediated by the copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and in situ click chemistry or conjunction with other techniques; druggability optimization with 1,2,3-triazole groups; and intracellular self-assembly platforms with ring tension reactions, which are presented from the viewpoint of drug development. There is a reasonable prospect that bioorthogonal coupling reactions will accelerate the screening of lead compounds, the designing strategies of small molecules and expand the variety of designed compounds, which will be a new trend in drug development in the future.
Collapse
|
5
|
Krishna Sunkari Y, Kumar Siripuram V, Flajolet M. Diversity-Oriented Synthesis (DOS) of On-DNA Peptidomimetics from Acid-Derived Phosphonium Ylides. Chemistry 2023; 29:e202203037. [PMID: 36653313 DOI: 10.1002/chem.202203037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 01/20/2023]
Abstract
The DNA-encoded library (DEL) technology represents a revolutionary drug-discovery tool with unprecedented screening power originating from the association of combinatorial chemistry and DNA barcoding. The chemical diversity of DELs and its chemical space will be further expanded as new DNA-compatible reactions are introduced. This work introduces the use of DOS in the context of on-DNA peptidomimetics. Wittig olefination of aspartic acid-derived on-DNA Wittig ylide, combined with a broad substrate scope of aldehydes, led to formation of on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated ketones. The synthesis of on-DNA multi-peptidyl-ylides was performed by incorporating sequential amino acids onto a monomeric ylide. Di-, tri- and tetrameric peptidyl-ylides were validated for Wittig olefination and led to on-DNA α ${\alpha }$ , β ${\beta }$ -unsaturated-based peptidomimetics, an important class of intermediates. One on-DNA aryl Wittig ylide was also developed and applied to Wittig olefination for synthesis of on-DNA chalcone-based molecules. Furthermore, DOS was used successfully with electron-deficient peptidomimetics and led to the development of different heterocyclic cores containing on-DNA peptidomimetics.
Collapse
Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| |
Collapse
|
6
|
Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
| |
Collapse
|
7
|
Škopić MK, Dos Santos Smith D, Gohla A, Kunig VBK, Brunschweiger A. Initiating DNA-Encoded Library Synthesis with a Hexathymidine DNA Oligonucleotide. Methods Mol Biol 2022; 2541:89-104. [PMID: 36083549 DOI: 10.1007/978-1-0716-2545-3_14] [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
Libraries of DNA-encoded compounds (DELs) are a validated screening technology for drug discovery. Here we describe a library synthesis strategy that starts with a solid phase-bound, chemically very stable hexathymidine DNA sequence "hexT." Different heterocycle conjugates of the hexT oligonucleotide were synthesized from simple starting materials using metal or acid catalysts. The hexT conjugates were isolated, characterized, and ligated to coding DNA sequences.
Collapse
Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | | | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany.
| |
Collapse
|
8
|
Graham JS, Hunter JH, Waring MJ. Micellar Buchwald-Hartwig Coupling of Aryl and Heteroarylamines for the Synthesis of DNA-Encoded Libraries. J Org Chem 2021; 86:17257-17264. [PMID: 34788051 DOI: 10.1021/acs.joc.1c02325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA-encoded libraries are a very efficient means of identifying ligands for protein targets in high throughput. To fully maximize their use, it is essential to be able to carry out efficient reactions on DNA-conjugated substrates. Arylamines are privileged motifs in druglike molecules, and methods for their incorporation into DNA-encoded libraries are highly desirable. One of the preferred methods for their preparation, the Buchwald-Hartwig coupling, does not perform well on DNA conjugates using current approaches. We report the application of our recently developed micellar technology for on-DNA chemistry to the Buchwald-Hartwig reaction. Optimization of conditions led to a robust, high-yielding method for the synthesis of DNA-conjugated aryl and heteroarylamines, which is broad in substrate scope for both the arylamine and the DNA-conjugated aryl halide and is fully compatible with DNA-encoding and decoding procedures. This method will enable the preparation of diverse, high-fidelity libraries of biarylamines.
Collapse
Affiliation(s)
- Jessica S Graham
- 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
| | - 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
| | - 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
| |
Collapse
|
9
|
Zhang J, Li X, Wei H, Li Y, Zhang G, Li Y. Sequential DNA-Encoded Building Block Fusion for the Construction of Polysubstituted Pyrazoline Core Libraries. Org Lett 2021; 23:8429-8433. [PMID: 34652930 DOI: 10.1021/acs.orglett.1c03145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The construction of chemical libraries containing polysubstituted pyrazoline scaffolds is highly desirable for the discovery of novel chemical ligands for biological targets. Herein, we report a sequential DNA-encoded synthesis strategy for polysubstituted pyrazoline heterocycles, which fuses a broad panel of aldehydes, aryl amines, and alkenes as building blocks. Furthermore, mock library synthesis and selection demonstrated the ability of the method to produce DNA-encoded focused libraries with highly functionalized pyrazoline cores.
Collapse
Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Haimei Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
| | - Ryan T Walsh
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | | |
Collapse
|
11
|
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
Collapse
Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Hunter JH, Anderson MJ, Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Crawford JJ, Madin A, Pairaudeau G, Waring MJ. Highly efficient on-DNA amide couplings promoted by micelle forming surfactants for the synthesis of DNA encoded libraries. Chem Sci 2021; 12:9475-9484. [PMID: 34349922 PMCID: PMC8278914 DOI: 10.1039/d1sc03007h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
DNA encoded libraries (DELs) represent powerful new technology for finding small molecule ligands for proteins and are increasingly being applied to hit finding in medicinal chemistry. Crucial to the synthesis of high quality DELs is the identification of chemical reactions for their assembly that proceed with very high conversion across a range of different substrates, under conditions compatible with DNA-tagged substrates. Many current chemistries used in DEL synthesis do not meet this requirement, resulting in libraries of low fidelity. Amide couplings are the most commonly used reaction in synthesis of screening libraries and also in DELs. The ability to carry out highly efficient, widely applicable amide couplings in DEL synthesis would therefore be highly desirable. We report a method for amide coupling using micelle forming surfactants, promoted by a modified linker, that is broadly applicable across a wide range of substrates. Most significantly, this works exceptionally well for coupling of DNA-conjugated carboxylic acids (N-to-C) with amines in solution, a procedure that is currently very inefficient. The optimisation of separate procedures for coupling of DNA-conjugated acids and amines by reagent screening and statistically driven optimisation is described. The generality of the method is illustrated by the application to a wide range of examples with unprecedented levels of conversion. The utility of the (N-to-C) coupling of DNA-conjugated acids in DEL synthesis is illustrated by the three cycle synthesis of a fully DNA-encoded compound by two cycles of coupling of an aminoester, with intermediate ester hydrolysis, followed by capping with an amine. This methodology will be of great utility in the synthesis of high fidelity DELs.
Collapse
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 UK
| | - Matthew J Anderson
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - 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 UK
| | - James J Crawford
- Department of Discovery Chemistry, Genentech Inc. 1 DNA Way South San Francisco CA 94080 USA
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Garry Pairaudeau
- Exscientia Schrödinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - 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 UK
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Shi Y, Wu YR, Yu JQ, Zhang WN, Zhuang CL. DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output. RSC Adv 2021; 11:2359-2376. [PMID: 35424149 PMCID: PMC8693808 DOI: 10.1039/d0ra09889b] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
A DNA-encoded library is a collection of small molecules covalently linked to DNA that has unique information about the identity and the structure of each library member. A DNA-encoded chemical library (DEL) is broadly adopted by major pharmaceutical companies and used in numerous drug discovery programs. The application of the DEL technology is advantageous at the initial period of drug discovery because of reduced cost, time, and storage space for the identification of target compounds. The key points for the construction of DELs comprise the development and the selection of the encoding methods, transfer of routine chemical reaction from off-DNA to on-DNA, and exploration of new chemical reactions on DNA. The limitations in the chemical space and the diversity of DEL were reduced gradually by using novel DNA-compatible reactions based on the formation and the cleavage of various bonds. Here, we summarized a series of novel DNA-compatible chemistry reactions for DEL building blocks and analysed the druggability of screened hit molecules via DELs in the past five years.
Collapse
Affiliation(s)
- Ying Shi
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Yan-Ran Wu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Jian-Qiang Yu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Wan-Nian Zhang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| | - Chun-Lin Zhuang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| |
Collapse
|
19
|
Kunig VBK, Potowski M, Akbarzadeh M, Klika Škopić M, dos Santos Smith D, Arendt L, Dormuth I, Adihou H, Andlovic B, Karatas H, Shaabani S, Zarganes‐Tzitzikas T, Neochoritis CG, Zhang R, Groves M, Guéret SM, Ottmann C, Rahnenführer J, Fried R, Dömling A, Brunschweiger A. TEAD-YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics. Angew Chem Int Ed Engl 2020; 59:20338-20342. [PMID: 32537835 PMCID: PMC7689693 DOI: 10.1002/anie.202006280] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/20/2020] [Indexed: 01/12/2023]
Abstract
DNA-encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or "hot spot", regions of protein-protein interactions. A DNA-encoded combinatorial peptoid library was designed based on the Ugi four-component reaction by employing tryptophan-mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide "hexT", encoded by DNA sequences, and substituted by azide-alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor-relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD-YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.
Collapse
Affiliation(s)
- Verena B. K. Kunig
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Marco Potowski
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Mohammad Akbarzadeh
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Mateja Klika Škopić
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Denise dos Santos Smith
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Lukas Arendt
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Ina Dormuth
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM)BioPharmaceuticals R&DAstraZeneca43150GothenburgSweden
- AstraZeneca-Max Planck Institute Satellite UnitMax-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Blaž Andlovic
- Lead Discovery Center GmbH (Germany)Otto-Hahn-Strasse 1544227DortmundGermany
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering and Institute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Hacer Karatas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Shabnam Shaabani
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | | | - Constantinos G. Neochoritis
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
- University of CreteDepartment of Chemistry70013HeraklionGreece
| | - Ran Zhang
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Matthew Groves
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Stéphanie M. Guéret
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM)BioPharmaceuticals R&DAstraZeneca43150GothenburgSweden
- AstraZeneca-Max Planck Institute Satellite UnitMax-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Christian Ottmann
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering and Institute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Jörg Rahnenführer
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Roland Fried
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Alexander Dömling
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Andreas Brunschweiger
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| |
Collapse
|
20
|
Kunig VBK, Potowski M, Akbarzadeh M, Klika Škopić M, Santos Smith D, Arendt L, Dormuth I, Adihou H, Andlovic B, Karatas H, Shaabani S, Zarganes‐Tzitzikas T, Neochoritis CG, Zhang R, Groves M, Guéret SM, Ottmann C, Rahnenführer J, Fried R, Dömling A, Brunschweiger A. TEAD–YAP Interaction Inhibitors and MDM2 Binders from DNA‐Encoded Indole‐Focused Ugi Peptidomimetics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Verena B. K. Kunig
- TU Dortmund University Faculty of Chemistry and Chemical Biology Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Marco Potowski
- TU Dortmund University Faculty of Chemistry and Chemical Biology Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Mohammad Akbarzadeh
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Mateja Klika Škopić
- TU Dortmund University Faculty of Chemistry and Chemical Biology Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Denise Santos Smith
- TU Dortmund University Faculty of Chemistry and Chemical Biology Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Lukas Arendt
- TU Dortmund University Faculty of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Ina Dormuth
- TU Dortmund University Faculty of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM) BioPharmaceuticals R&D AstraZeneca 43150 Gothenburg Sweden
- AstraZeneca-Max Planck Institute Satellite Unit Max-Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Blaž Andlovic
- Lead Discovery Center GmbH (Germany) Otto-Hahn-Strasse 15 44227 Dortmund Germany
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Hacer Karatas
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Shabnam Shaabani
- University of Groningen Drug Design Deusinglaan 1 7313 AV Groningen The Netherlands
| | | | - Constantinos G. Neochoritis
- University of Groningen Drug Design Deusinglaan 1 7313 AV Groningen The Netherlands
- University of Crete Department of Chemistry 70013 Heraklion Greece
| | - Ran Zhang
- University of Groningen Drug Design Deusinglaan 1 7313 AV Groningen The Netherlands
| | - Matthew Groves
- University of Groningen Drug Design Deusinglaan 1 7313 AV Groningen The Netherlands
| | - Stéphanie M. Guéret
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM) BioPharmaceuticals R&D AstraZeneca 43150 Gothenburg Sweden
- AstraZeneca-Max Planck Institute Satellite Unit Max-Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Jörg Rahnenführer
- TU Dortmund University Faculty of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Roland Fried
- TU Dortmund University Faculty of Statistics Vogelpothsweg 87 44227 Dortmund Germany
| | - Alexander Dömling
- University of Groningen Drug Design Deusinglaan 1 7313 AV Groningen The Netherlands
| | - Andreas Brunschweiger
- TU Dortmund University Faculty of Chemistry and Chemical Biology Otto-Hahn-Strasse 6 44227 Dortmund Germany
| |
Collapse
|
21
|
Li K, Liu X, Liu S, An Y, Shen Y, Sun Q, Shi X, Su W, Cui W, Duan Z, Kuai L, Yang H, Satz AL, Chen K, Jiang H, Zheng M, Peng X, Lu X. Solution-Phase DNA-Compatible Pictet-Spengler Reaction Aided by Machine Learning Building Block Filtering. iScience 2020; 23:101142. [PMID: 32446221 PMCID: PMC7243192 DOI: 10.1016/j.isci.2020.101142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 02/05/2023] Open
Abstract
The application of machine learning toward DNA encoded library (DEL) technology is lacking despite obvious synergy between these two advancing technologies. Herein, a machine learning algorithm has been developed that predicts the conversion rate for the DNA-compatible reaction of a building block with a model DNA-conjugate. We exemplify the value of this technique with a challenging reaction, the Pictet-Spengler, where acidic conditions are normally required to achieve the desired cyclization between tryptophan and aldehydes to provide tryptolines. This is the first demonstration of using a machine learning algorithm to cull potential building blocks prior to their purchase and testing for DNA-encoded library synthesis. Importantly, this allows for a challenging reaction, with an otherwise very low building block pass rate in the test reaction, to still be used in DEL synthesis. Furthermore, because our protocol is solution phase it is directly applicable to standard plate-based DEL synthesis.
Collapse
Affiliation(s)
- Ke Li
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaohong Liu
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - 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, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yulong An
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yanfang Shen
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qingxia Sun
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhiqiang Duan
- 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, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Letian Kuai
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L Satz
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Kaixian Chen
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, 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, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| |
Collapse
|
22
|
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.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Ruff Y, Martinez R, Pellé X, Nimsgern P, Fille P, Ratnikov M, Berst F. An Amphiphilic Polymer-Supported Strategy Enables Chemical Transformations under Anhydrous Conditions for DNA-Encoded Library Synthesis. ACS COMBINATORIAL SCIENCE 2020; 22:120-128. [PMID: 32040908 DOI: 10.1021/acscombsci.9b00164] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of DNA-encoded libraries has emerged as a powerful hit generation technology. Combining the power of combinatorial chemistry to enumerate large compound collections with the efficiency of affinity selection in pools, the methodology makes it possible to interrogate vast chemical space against biological targets of pharmaceutical relevance. Thus, the chemical transformations employed for the synthesis of encoded libraries play a crucial role in the identification of diverse and drug-like starting points. Currently established transformations have mostly been limited to water-compatible reactions to accommodate the growing oligonucleotide tag. Herein, we describe the development of a practical catch-and-release methodology utilizing a cationic, amphiphilic PEG-based polymer to perform chemical transformations on immobilized DNA conjugates under anhydrous conditions. We demonstrate the usefulness of our APTAC (amphiphilic polymer-facilitated transformations under anhydrous conditions) approach by performing several challenging transformations on DNA-conjugated small molecules in pure organic solvents: the addition of a carbanion equivalent to a DNA-conjugated ketone in tetrahydrofuran, the synthesis of saturated heterocycles using the tin (Sn) amine protocol (SnAP) in dichloromethane, and the dual-catalytic (Ir/Ni) metallaphotoredox decarboxylative cross-coupling of carboxylic acids to DNA-conjugated aryl halides in DMSO. In addition, we demonstrate the feasibility of the latter in multititer-plate format.
Collapse
Affiliation(s)
- Yves Ruff
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Roberto Martinez
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Pierre Nimsgern
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Pascale Fille
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Maxim Ratnikov
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| |
Collapse
|
25
|
Zambaldo C, Geigle SN, Satz AL. High-Throughput Solid-Phase Building Block Synthesis for DNA-Encoded Libraries. Org Lett 2019; 21:9353-9357. [PMID: 31747291 DOI: 10.1021/acs.orglett.9b03553] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we provide a generalizable method for the cost-effective synthesis of thousands of building blocks (BBs) employing DNA-incompatible chemistries. The ability to produce large numbers of crude products via solid-phase synthesis has existed for decades; however, our work demonstrates a practical use of such crude reaction mixtures and employs DNA-conjugation to simultaneously encode, purify, and rapidly analyze the desired products. This workflow generated sp3-rich BBs that could be encoded by DNA in a high-throughput manner.
Collapse
|
26
|
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.
Collapse
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 .
| |
Collapse
|
27
|
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]
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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.
Collapse
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 .
| |
Collapse
|
30
|
Škopić MK, Götte K, Gramse C, Dieter M, Pospich S, Raunser S, Weberskirch R, Brunschweiger A. Micellar Brønsted Acid Mediated Synthesis of DNA-Tagged Heterocycles. J Am Chem Soc 2019; 141:10546-10555. [PMID: 31244181 DOI: 10.1021/jacs.9b05696] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The translation of well-established molecular biology methods such as genetic coding, selection, and DNA sequencing to combinatorial organic chemistry and compound identification has made extremely large compound collections, termed DNA-encoded libraries, accessible for drug screening. However, the reactivity of the DNA imposes limitations on the choice of chemical methods for encoded library synthesis. For example, strongly acidic reaction conditions must be avoided because they damage the DNA by depurination, i.e. the cleavage of purine bases from the oligomer. Application of micellar catalysis holds much promise for encoded chemistry. Aqueous micellar dispersions enabled compound synthesis under often appealingly mild conditions. Amphiphilic block copolymers covalently functionalized with sulfonic acid moieties in the lipophilic portion assemble in water and locate the Brønsted catalyst in micelles. These acid nanoreactors enabled the reaction of DNA-conjugated aldehydes to diverse substituted tetrahydroquinolines and aminoimidazopyridines by Povarov and Groebke-Blackburn-Bienaymé reactions, respectively, and the cleavage of tBoc protective groups from amines. The polymer micelle design was successfully translated to the Cu/Bipyridine/TEMPO system mediating the oxidation of DNA-coupled alcohols to the corresponding aldehydes. These results suggest a potentially broad applicability of polymer micelles for encoded chemistry.
Collapse
Affiliation(s)
- M Klika Škopić
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - K Götte
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - C Gramse
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - M Dieter
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - S Pospich
- Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 Dortmund , Germany
| | - S Raunser
- Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 Dortmund , Germany
| | - R Weberskirch
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - A Brunschweiger
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| |
Collapse
|
31
|
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
| |
Collapse
|
32
|
Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
Collapse
Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | | |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Du HC, Simmons N, Faver JC, Yu Z, Palaniappan M, Riehle K, Matzuk MM. A Mild, DNA-Compatible Nitro Reduction Using B 2(OH) 4. Org Lett 2019; 21:2194-2199. [PMID: 30860855 PMCID: PMC6457042 DOI: 10.1021/acs.orglett.9b00497] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
A hypodiboric
acid system for the reduction of nitro groups on
DNA–chemical conjugates has been developed. This transformation
provided good to excellent yields of the reduced amine product for
a variety of functionalized aromatic, heterocyclic, and aliphatic
nitro compounds. DNA tolerance to reaction conditions, extension to
decigram scale reductions, successful use in a DNA-encoded chemical
library synthesis, and subsequent target selection are also described.
Collapse
Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - John C Faver
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Zhifeng Yu
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Murugesan Palaniappan
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kevin Riehle
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery , Baylor College of Medicine , Houston , Texas 77030 , United States
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Wang X, Sun H, Liu J, Zhong W, Zhang M, Zhou H, Dai D, Lu X. Palladium-Promoted DNA-Compatible Heck Reaction. Org Lett 2019; 21:719-723. [DOI: 10.1021/acs.orglett.8b03926] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- 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, P.R. China
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Hui Sun
- 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, P.R. China
| | - Jiaxiang 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, P.R. China
| | - Wenge Zhong
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Mingqiang Zhang
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. China
| | - Hu Zhou
- 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, P.R. China
| | - Dongcheng Dai
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Company, Limited, 4560 Jinke Road, Building No. 2, 13th Floor, Pudong, Shanghai 201210, P.R. 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, P.R. China
| |
Collapse
|
37
|
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: 35] [Impact Index Per Article: 5.8] [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.
Collapse
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
| |
Collapse
|
38
|
Favalli N, Bassi G, Scheuermann J, Neri D. DNA-encoded chemical libraries - achievements and remaining challenges. FEBS Lett 2018; 592:2168-2180. [PMID: 29683493 PMCID: PMC6126621 DOI: 10.1002/1873-3468.13068] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 11/10/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
Collapse
Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| |
Collapse
|
39
|
Valeur E, Jimonet P. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm. J Med Chem 2018; 61:9004-9029. [DOI: 10.1021/acs.jmedchem.8b00378] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eric Valeur
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Patrick Jimonet
- External Innovation Drug Discovery, Global Business Development & Licensing, Sanofi, 13 quai Jules Guesde, 94400 Vitry-sur-Seine, France
| |
Collapse
|
40
|
Probst D, Heitz M, Poirier M, Gan BH, Delalande C, Reymond JL. Frontiers in Medicinal Chemistry 2017 in Bern, Switzerland. ChemMedChem 2017; 12:1645-1651. [PMID: 28941184 DOI: 10.1002/cmdc.201700306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/06/2022]
Abstract
Sharing capital ideas: The 2017 Frontiers in Medicinal Chemistry (FiMC) conference, organized jointly by the German Chemical Society, the German Pharmaceutical Society, and the Swiss Chemical Society, was held at the Department of Chemistry and Biochemistry of the University of Bern in February 2017. Herein we summarize the many conference highlights, and look forward to the next FiMC meeting, to be held in Jena (Germany) in March 2018.
Collapse
Affiliation(s)
- Daniel Probst
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marc Heitz
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marion Poirier
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Bee Ha Gan
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Clémence Delalande
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Jean-Louis Reymond
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|