1
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Anderson MJ, Carton TP, Salvini CLA, Crawford JJ, Pairaudeau G, Waring MJ. Micelle-Promoted Reductive Amination of DNA-Conjugated Amines for DNA-Encoded Library Synthesis. Chemistry 2024; 30:e202400239. [PMID: 38251309 DOI: 10.1002/chem.202400239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/23/2024]
Abstract
DNA-encoded libraries (DELs) have become a leading technology for hit identification in drug discovery projects as large, diverse libraries can be generated. DELs are commonly synthesised via split-and-pool methodology; thus, chemical transformations utilised must be highly efficient, proceeding with high conversions. Reactions performed in DEL synthesis also require a broad substrate scope to produce diverse, drug-like libraries. Many pharmaceutical compounds incorporate multiple C-N bonds, over a quarter of which are synthesised via reductive aminations. However, few on-DNA reductive amination procedures have been developed. Herein is reported the application of the micelle-forming surfactant, TPGS-750-M, to the on-DNA reductive amination of DNA-conjugated amines, yielding highly efficient conversions with a broad range of aldehydes, including medicinally relevant heterocyclic and aliphatic substrates. The procedure is compatible with DNA amplification and sequencing, demonstrating its applicability to DEL synthesis.
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Affiliation(s)
- 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
| | - Thomas P Carton
- 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
| | | | | | - 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
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2
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Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
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Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
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3
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Abstract
DNA-encoded libraries (DELs) are widely used in the discovery of drug candidates, and understanding their design principles is critical for accessing better libraries. Most DELs are combinatorial in nature and are synthesized by assembling sets of building blocks in specific topologies. In this study, different aspects of library topology were explored and their effect on DEL properties and chemical diversity was analyzed. We introduce a descriptor for DEL topological assignment (DELTA) and use it to examine the landscape of possible DEL topologies and their coverage in the literature. A generative topographic mapping analysis revealed that the impact of library topology on chemical space coverage is secondary to building block selection. Furthermore, it became apparent that the descriptor used to analyze chemical space dictates how structures cluster, with the effects of topology being apparent when using three-dimensional descriptors but not with common two-dimensional descriptors. This outcome points to potential challenges of attempts to predict DEL productivity based on chemical space analyses alone. While topology is rather inconsequential for defining the chemical space of encoded compounds, it greatly affects possible interactions with target proteins as illustrated in docking studies using NAD/NADP binding proteins as model receptors.
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Affiliation(s)
- William K Weigel
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, Utah 84112, United States
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4
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Zhang P, Koch G, Zhang Y, Yang K, Lokey RS. DNA-Compatible Conditions for the Formation of N-Methyl Peptide Bonds. ACS OMEGA 2023; 8:23477-23483. [PMID: 37426286 PMCID: PMC10323948 DOI: 10.1021/acsomega.3c00576] [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: 01/28/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
DNA-encoded libraries (DELs) are a powerful platform in drug discovery. Peptides have unique properties that make them attractive pharmaceutical candidates. N-methylation of the peptide backbone can confer beneficial properties such as increased proteolytic stability and membrane permeability. Herein, we evaluate different DEL reaction systems and report a DNA-compatible protocol for forming N-methylated amide bonds. The DNA-compatible, bis(trichloromethyl)carbonate-mediated amide coupling is efficient for the formation of N-methyl peptide bonds, which promises to increase the opportunity to identify passively cell-permeable macrocyclic peptide hits by DNA-encoded technology.
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Affiliation(s)
- Panpan Zhang
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Grant Koch
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Yankun Zhang
- College
of Letters and Science, University of California
Santa Barbara, Santa
Barbara, California 93106, United States
| | - Kevin Yang
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
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5
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Antisense Oligonucleotides Conjugated with Lipophilic Compounds: Synthesis and In Vitro Evaluation of Exon Skipping in Duchenne Muscular Dystrophy. Int J Mol Sci 2022; 23:ijms23084270. [PMID: 35457088 PMCID: PMC9032562 DOI: 10.3390/ijms23084270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Our groups previously reported that conjugation at 3′-end with ursodeoxycholic acid (UDCA) significantly enhanced in vitro exon skipping properties of ASO 51 oligonucleotide targeting the human DMD exon 51. In this study, we designed a series of lipophilic conjugates of ASO 51, to explore the influence of the lipophilic moiety on exon skipping efficiency. To this end, three bile acids and two fatty acids have been derivatized and/or modified and conjugated to ASO 51 by automatized solid phase synthesis. We measured the melting temperature (Tm) of lipophilic conjugates to evaluate their ability to form a stable duplex with the target RNA. The exon skipping efficiency has been evaluated in myogenic cell lines first in presence of a transfection agent, then in gymnotic conditions on a selection of conjugated ASO 51. In the case of 5′-UDC-ASO 51, we also evaluated the influence of PS content on exon skipping efficiency; we found that it performed better exon skipping with full PS linkages. The more efficient compounds in terms of exon skipping were found to be 5′-UDC- and 5′,3′-bis-UDC-ASO 51.
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6
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Adamik R, Buchholcz B, Darvas F, Sipos G, Novák Z. The Potential of Micellar Media in the Synthesis of DNA-Encoded Libraries. Chemistry 2022; 28:e202103967. [PMID: 35019168 PMCID: PMC9305553 DOI: 10.1002/chem.202103967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/17/2022]
Abstract
DNA‐encoded library (DEL) technology has become widely used in drug discovery research. The construction of DELs requires robust organic transformations that proceed in aqueous media under mild conditions. Unfortunately, the application of water as reaction medium for organic synthesis is not evident due to the generally limited solubility of organic reagents. However, the use of surfactants can offer a solution to this issue. Oil‐in‐water microemulsions formed by surfactant micelles are able to localize hydrophobic reagents inside them, resulting in high local concentrations of the organic substances in an otherwise poorly solvated environment. This review provides a conceptual and critical summary of micellar synthesis possibilities that are well suited to DEL synthesis. Existing examples of micellar DEL approaches, together with a selection of micellar organic transformations fundamentally suitable for DEL are discussed.
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Affiliation(s)
- Réka Adamik
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
| | | | - Ferenc Darvas
- Innostudio Inc., Záhony u. 7, 1031, Budapest, Hungary
| | | | - Zoltán Novák
- ELTE "Lendület" Catalysis and Organic Synthesis Research Group, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter stny. 1/A, 1117, Budapest, Hungary
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7
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Sun ZM, Yang SG, Xue LJ, Zhang J, Yang K, Hu YJ. N-Alkyl Linkers for DNA-Encoded Chemical Libraries. Chem Asian J 2022; 17:e202200016. [PMID: 35254005 DOI: 10.1002/asia.202200016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/14/2022] [Indexed: 11/06/2022]
Abstract
A series of novel N-alkyl linkers that connect small-molecule library members with their encoding DNA oligonucleotides has been developed. In comparison with the standard amide linker (usually constructed with oligo-AOP-NH2 ), the N-alkyl linker is not only more chemically stable, but also provides better structural diversity at the linkage point. Chemical variety in the vicinity of the polyglycol terminus, in particular, could affect binding interactions with the target protein. It could have been neglected in previous DNA-encoded chemical library (DEL) synthesis and screening studies due to the limited linkage alternatives. With these linkers, one can produce versatile key intermediates as Cycle 1 products directly amenable to Cycle 2 chemistry without the use of protecting groups. As a result, a DEL synthesis process that uses the fewest chemical conversions, such as 3-step, 3-cycle DELs, can achieve higher synthetic efficiency while creating less DNA tag degradation, resulting in higher quality DELs.
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Affiliation(s)
- Zhao-Mei Sun
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Shao-Guang Yang
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Li-Jun Xue
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Jie Zhang
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
| | - Kexin Yang
- Taihe Road, Pharmaron Beijing Co., Ltd., BDA, Beijing, 100176, P. R. China
| | - Yun-Jin Hu
- Pharmaron (Ningbo) Technology Development Co., Ltd. No. 800 Bin-Hai 4th Road, Hangzhou Bay New Zone, Ningbo, 315336, P. R. China
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8
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Chai J. On-DNA Reductive Amination and Alkylation. Methods Mol Biol 2022; 2541:33-37. [PMID: 36083540 DOI: 10.1007/978-1-0716-2545-3_5] [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
On-DNA reductive amination (on-DNA aldehyde with amine building blocks) and alkylation (on-DNA amine with aldehyde building blocks) are robust ways to form C-N bond. The large sets of commercially available aldehyde and amine building blocks make reductive amination and alkylation widely used in DEL synthesis.
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Affiliation(s)
- Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
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9
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Cai P, Schneider LA, Stress C, Gillingham D. Building Boron Heterocycles into DNA-Encoded Libraries. Org Lett 2021; 23:8772-8776. [PMID: 34723549 DOI: 10.1021/acs.orglett.1c03262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA-encoded library (DEL) technology uses DNA tags to track the synthetic history of individual members in a split-and-pool combinatorial synthesis scheme. DEL synthesis hinges on robust methodologies that tolerate combinatorial synthesis schemes while not destroying the information in DNA. We introduce here a DEL-compatible reaction that assembles a boron-containing pyridazine heterocycle. The heterocycle is unique because it can engage in reversible covalent interactions with alcohols─a feature that, until now, has not been deliberately engineered into DELs.
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Affiliation(s)
- Pinwen Cai
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Lukas A Schneider
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Cedric Stress
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
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10
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Zhang Y, Luo H, Ma H, Wan J, Ji Y, Shaginian A, Li J, Deng Y, Liu G. On-DNA Derivatization of Quinoxalin-2-ones by Visible-Light-Triggered Alkylation with Carboxylic Acids. Bioconjug Chem 2021; 32:1576-1580. [PMID: 34346691 DOI: 10.1021/acs.bioconjchem.1c00346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An efficient visible-light-induced alkylation of DNA-tagged quinoxaline-2-ones was described. The methodology demonstrated moderate-to-excellent conversions under mild conditions. The reaction was found to be tolerant with both N-protected α-amino acids and aliphatic carboxylic acids and could be applied to the synthesis of focused DNA-encoded quinoxalin-2-one libraries.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, P.R. China
| | - Huadong Luo
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Huiyong Ma
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Yue Ji
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Alex Shaginian
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Jin Li
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
| | - Yun Deng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, Sichuan, P.R. China
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610000, Sichuan, P.R. China
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11
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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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12
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Large screening of DNA-compatible reaction conditions for Suzuki and Sonogashira cross-coupling reactions and for reverse amide bond formation. Bioorg Med Chem 2021; 41:116206. [PMID: 34038862 DOI: 10.1016/j.bmc.2021.116206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/02/2023]
Abstract
Progress in DNA-encoded chemical library synthesis and screening crucially relies on the availability of DNA-compatible reactions, which proceed with high yields and excellent purity for a large number of possible building blocks. In the past, experimental conditions have been presented for the execution of Suzuki and Sonogashira cross-coupling reactions on-DNA. In this article, our aim was to optimize Suzuki and Sonogashira reactions, comparing our results to previously published procedures. We have tested the performance of improved conditions using 606 building blocks (including boronic acids, pinacol boranes and terminal alkynes), achieving >70% conversion for 84% of the tested molecules. Moreover, we describe efficient experimental conditions for the on-DNA synthesis of amide bonds, starting from DNA derivatives carrying a carboxylic acid moiety and 300 primary, secondary and aromatic amines, as amide bonds are frequently found in DNA-encoded chemical libraries thanks to their excellent DNA compatibility.
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13
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Wu R, Du T, Sun W, Shaginian A, Gao S, Li J, Wan J, Liu G. Functionalization of DNA-Tagged Alkenes Enabled by Visible-Light-Induced C–H Activation of N-Aryl Tertiary Amines. Org Lett 2021; 23:3486-3490. [DOI: 10.1021/acs.orglett.1c00924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rongfeng Wu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Tian Du
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Wenbo Sun
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Alex Shaginian
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Sen Gao
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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14
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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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15
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Wu R, Gao S, Du T, Cai K, Cheng X, Fan J, Feng J, Shaginian A, Li J, Wan J, Liu G. Exploring Aldol Reactions on DNA and Applications to Produce Diverse Structures: An Example of Expanding Chemical Space of DNA-Encoded Compounds by Diversity-Oriented Synthesis. Chem Asian J 2020; 15:4033-4037. [PMID: 33119184 DOI: 10.1002/asia.202001105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/19/2020] [Indexed: 12/27/2022]
Abstract
A DNA-encoded chemical library (DECL) is built with combinatorial chemistry, which works by bringing chemical fragments together to generate diverse structures. However, chemical diversity of DNA-encoded chemical libraries is often limited by DNA compatible synthetic reactions. This report shows a conceptual strategy to expand chemical space of DNA-encoded chemical libraries by incorporation of diversity-oriented synthesis in DECL synthesis. We developed Aldol reactions on DNA in a combinatorial way. After obtaining DNA-tagged α, β-unsaturated ketones which represent important chemical intermediates, many distinct structures with skeletal diversities are achieved by diversity-oriented synthesis.
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Affiliation(s)
- Rongfeng Wu
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Sen Gao
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Tian Du
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Kunliang Cai
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Xuemin Cheng
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Jing Fan
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Jing Feng
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Alex Shaginian
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Jin Li
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
| | - Guansai Liu
- HitGen Inc. Building 6, No 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, P. R. China
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16
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Bao Y, Deng Z, Feng J, Zhu W, Li J, Wan J, Liu G. A B 2(OH) 4-Mediated Synthesis of 2-Substituted Indazolone and Its Application in a DNA-Encoded Library. Org Lett 2020; 22:6277-6282. [PMID: 32806212 DOI: 10.1021/acs.orglett.0c02032] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indazolone cores are among the most common structural components in medicinal chemistry and can be found in many biologically active molecules. In this report, a mild and efficient approach to 2-substituted indazolones via B2(OH)4-mediated reductive N-N bond formation is developed. This strategy features mild conditions, no request for a metal catalyst, and a wide scope for both aliphatic and aromatic amines. Meanwhile, this method was further successfully applied on DNA to construct indazolone cores for a DNA-encoded library. This will enable the production of a very attractive indazolone-cored library from simple amines and scaffolds, which will provide considerable diversity.
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Affiliation(s)
- Yapeng Bao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Zongfa Deng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Weiwei Zhu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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17
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DiRico K, Hua W, Liu C, Tucker JW, Ratnayake AS, Flanagan ME, Troutman MD, Noe MC, Zhang H. Ultra-High-Throughput Acoustic Droplet Ejection-Open Port Interface-Mass Spectrometry for Parallel Medicinal Chemistry. ACS Med Chem Lett 2020; 11:1101-1110. [PMID: 32550988 PMCID: PMC7294554 DOI: 10.1021/acsmedchemlett.0c00066] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
High-throughput experimentation (HTE) has emerged as an important tool in drug discovery, providing a platform for preparing large compound libraries and enabling swift reaction screening over wide-ranging conditions. Recent advances in automated high-density, material-sparing HTE have necessitated the development of rapid analytics with sensitivity and resolution sufficient to identify products and/or assess reaction performance in a timely and data-rich manner. Combination of an ultrathroughput (UT) reader platform with Acoustic Droplet Ejection-Open Port Interface-Mass Spectrometry (ADE-OPI-MS) provides the requisite speed and sensitivity. Herein, we report the application of ADE-OPI-MS to HTE in the areas of parallel medicinal chemistry and reaction screening.
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Affiliation(s)
- Kenneth
J. DiRico
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Wenyi Hua
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Joseph W. Tucker
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anokha S. Ratnayake
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew D. Troutman
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark C. Noe
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hui Zhang
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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18
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Bassi G, Favalli N, Oehler S, Martinelli A, Catalano M, Scheuermann J, Neri D. Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format. Biochem Biophys Res Commun 2020; 533:223-229. [PMID: 32386812 DOI: 10.1016/j.bbrc.2020.04.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/23/2022]
Abstract
DNA-encoded chemical libraries (DEL) are increasingly being used for the discovery and optimization of small organic ligands to proteins of biological or pharmaceutical interest. The DNA fragments, that serve as amplifiable identification barcodes for individual compounds in the library, are typically used in double-stranded DNA format. To the best of our knowledge, a direct comparison of DEL selections featuring DNA in either single- or double-stranded DNA format has not yet been reported. In this article, we describe a comparative evaluation of selections with two DEL libraries (named GB-DEL and NF-DEL), based on different chemical designs and produced in both single- and double-stranded DNA format. The libraries were selected in identical conditions against multiple protein targets, revealing comparable and reproducible fingerprints for both types of DNA formats. Surprisingly, selections performed with single-stranded DNA barcodes exhibited improved enrichment factors compared to double-stranded DNA. Using high-affinity ligands to carbonic anhydrase IX as benchmarks for selection performance, we observed an improved selectivity for the NF-DEL library (on average 2-fold higher enrichment factors) in favor of single-stranded DNA. The enrichment factors were even higher for the GB-DEL selections (approximately 5-fold), compared to the same library in double-stranded DNA format. Collectively, these results indicate that DEL libraries can conveniently be synthesized and screened in both single- and double-stranded DNA format, but single-stranded DNA barcodes typically yield enhanced enrichment factors.
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Affiliation(s)
- Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Sebastian Oehler
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Adriano Martinelli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Marco Catalano
- 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.
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19
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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20
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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: 15] [Impact Index Per Article: 3.8] [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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21
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Bobers J, Škopić MK, Dinter R, Sakthithasan P, Neukirch L, Gramse C, Weberskirch R, Brunschweiger A, Kockmann N. Design of an Automated Reagent-Dispensing System for Reaction Screening and Validation with DNA-Tagged Substrates. ACS COMBINATORIAL SCIENCE 2020; 22:101-108. [PMID: 32053337 DOI: 10.1021/acscombsci.9b00207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Laboratory automation strategies have vast potential for accelerating discovery processes. They enable higher efficiency and throughput for time-consuming screening procedures and reduce error-prone manual steps. Automating repetitive procedures can for instance support chemists in optimizing chemical reactions. Particularly, the technology of DNA-encoded libraries (DELs) may benefit from automation techniques, since translation of chemical reactions to DNA-tagged reactants often requires screening of multiple reaction parameters and evaluation of large numbers of reactants. Here, we describe a portable, automated system for reagent dispensing that was designed from open source materials. The system was validated by performing amide coupling of carboxylic acids to DNA-linked amine and a micelle-mediated Povarov reaction to DNA-tagged hexahydropyrroloquinolines. The latter reaction required accurate pipetting of multiple components including different solvents and a surface-active reagent. Analysis of reactions demonstrated that the robotic system achieved high accuracy comparable to experimentation by an experienced chemist with the potential of higher throughput.
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Affiliation(s)
- Jens Bobers
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Mateja Klika Škopić
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Robin Dinter
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Piriyanth Sakthithasan
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Laura Neukirch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Christian Gramse
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Ralf Weberskirch
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Norbert Kockmann
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
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22
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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23
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Su L, Feng J, Peng T, Wan J, Fan J, Li J, O’Connell J, Lancia DR, Franklin GJ, Liu G. Synthesis of Multifunctional 2-Aminobenzimidazoles on DNA via Iodine-Promoted Cyclization. Org Lett 2020; 22:1290-1294. [DOI: 10.1021/acs.orglett.9b04578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liqiang Su
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Ting Peng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Fan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jonathan O’Connell
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - David R. Lancia
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - G. Joseph Franklin
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
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24
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Liu W, Deng W, Sun S, Yu C, Su X, Wu A, Yuan Y, Ma Z, Li K, Yang H, Peng X, Dietrich J. A Strategy for the Synthesis of Sulfonamides on DNA. Org Lett 2019; 21:9909-9913. [DOI: 10.1021/acs.orglett.9b03843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wei Liu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Wei Deng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Saisai Sun
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Chunyan Yu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xubo Su
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Aliang Wu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Youlang Yuan
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Zhonglin Ma
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Ke Li
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Justin Dietrich
- Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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25
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Kunig VBK, Ehrt C, Dömling A, Brunschweiger A. Isocyanide Multicomponent Reactions on Solid-Phase-Coupled DNA Oligonucleotides for Encoded Library Synthesis. Org Lett 2019; 21:7238-7243. [PMID: 31464126 DOI: 10.1021/acs.orglett.9b02448] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isocyanide multicomponent reactions play a prominent role in drug discovery. This chemistry has hardly been investigated for compatibility with DNA-encoded combinatorial synthesis. The Ugi, Ugi-azide, and Groebke-Blackburn-Bienaymé reactions are well-tolerated by DNA on the solid phase and show a broad scope. However, an oxadiazole-forming variant of the Ugi reaction caused DNA depurination, requiring a more stable hexathymidine DNA for encoded library synthesis. Cheminformatic analysis revealed that isocyanide multicomponent-reaction-based encoded libraries cover a diverse chemical space.
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Affiliation(s)
- Verena B K Kunig
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Alexander Dömling
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
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26
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Cai P, Yang G, Zhao L, Wan J, Li J, Liu G. Synthesis of C3-Alkylated Indoles on DNA via Indolyl Alcohol Formation Followed by Metal-Free Transfer Hydrogenation. Org Lett 2019; 21:6633-6637. [DOI: 10.1021/acs.orglett.9b02132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pinwen Cai
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guanyu Yang
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Lanzhou Zhao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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27
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Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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28
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Flood DT, Asai S, Zhang X, Wang J, Yoon L, Adams ZC, Dillingham BC, Sanchez BB, Vantourout JC, Flanagan ME, Piotrowski DW, Richardson P, Green SA, Shenvi RA, Chen JS, Baran PS, Dawson PE. Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support. J Am Chem Soc 2019; 141:9998-10006. [PMID: 31136164 PMCID: PMC7033622 DOI: 10.1021/jacs.9b03774] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA Encoded Libraries have proven immensely powerful tools for lead identification. The ability to screen billions of compounds at once has spurred increasing interest in DEL development and utilization. Although DEL provides access to libraries of unprecedented size and diversity, the idiosyncratic and hydrophilic nature of the DNA tag severely limits the scope of applicable chemistries. It is known that biomacromolecules can be reversibly, noncovalently adsorbed and eluted from solid supports, and this phenomenon has been utilized to perform synthetic modification of biomolecules in a strategy we have described as reversible adsorption to solid support (RASS). Herein, we present the adaptation of RASS for a DEL setting, which allows reactions to be performed in organic solvents at near anhydrous conditions opening previously inaccessible chemical reactivities to DEL. The RASS approach enabled the rapid development of C(sp2)-C(sp3) decarboxylative cross-couplings with broad substrate scope, an electrochemical amination (the first electrochemical synthetic transformation performed in a DEL context), and improved reductive amination conditions. The utility of these reactions was demonstrated through a DEL-rehearsal in which all newly developed chemistries were orchestrated to afford a compound rich in diverse skeletal linkages. We believe that RASS will offer expedient access to new DEL reactivities, expanded chemical space, and ultimately more drug-like libraries.
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Affiliation(s)
- Dillon T. Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shota Asai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xuejing Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jie Wang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Leonard Yoon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Blythe C. Dillingham
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brittany B. Sanchez
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mark E. Flanagan
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - David W. Piotrowski
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive, San Diego, CA 92121, United States
| | - Samantha A. Green
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Stress CJ, Sauter B, Schneider LA, Sharpe T, Gillingham D. A DNA-Encoded Chemical Library Incorporating Elements of Natural Macrocycles. Angew Chem Int Ed Engl 2019; 58:9570-9574. [PMID: 30938482 DOI: 10.1002/anie.201902513] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/01/2019] [Indexed: 12/22/2022]
Abstract
Here we show a seven-step chemical synthesis of a DNA-encoded macrocycle library (DEML) on DNA. Inspired by polyketide and mixed peptide-polyketide natural products, the library was designed to incorporate rich backbone diversity. Achieving this diversity, however, comes at the cost of the custom synthesis of bifunctional building block libraries. This study outlines the importance of careful retrosynthetic design in DNA-encoded libraries, while revealing areas where new DNA synthetic methods are needed.
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Affiliation(s)
- Cedric J Stress
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Basilius Sauter
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Lukas A Schneider
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
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30
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Stress CJ, Sauter B, Schneider LA, Sharpe T, Gillingham D. Eine DNA‐kodierte Molekülbibliothek mit Elementen natürlicher Makrocyclen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902513] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Cedric J. Stress
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Basilius Sauter
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Lukas A. Schneider
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Timothy Sharpe
- Biophysikalisches InstitutBiozentrumUniversität Basel Klingelbergstrasse 50/70 4056 Basel Schweiz
| | - Dennis Gillingham
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
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31
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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32
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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33
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Li Y, De Luca R, Cazzamalli S, Pretto F, Bajic D, Scheuermann J, Neri D. Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold. Nat Chem 2018; 10:441-448. [PMID: 29556050 PMCID: PMC6044424 DOI: 10.1038/s41557-018-0017-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 01/04/2018] [Indexed: 11/09/2022]
Abstract
In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor. Similar to antibodies, the encoded display of multiple chemical elements on a constant scaffold enabled practical applications, such as fluorescence microscopy procedures or the selective in vivo delivery of payloads to tumours. Furthermore, the versatile structure of the scaffold facilitated the generation of protein-specific chemical probes, as illustrated by photo-crosslinking.
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Affiliation(s)
- Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Shapingba, Chongqing, China
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Roberto De Luca
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Samuele Cazzamalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | | | - Davor Bajic
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
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34
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Lu X, Fan L, Phelps CB, Davie CP, Donahue CP. Ruthenium Promoted On-DNA Ring-Closing Metathesis and Cross-Metathesis. Bioconjug Chem 2017; 28:1625-1629. [DOI: 10.1021/acs.bioconjchem.7b00292] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaojie Lu
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Lijun Fan
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christopher B. Phelps
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christopher P. Davie
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Christine P. Donahue
- GlaxoSmithKline, Platform Technology & Science, Drug Discovery and Selection, New Chemical Entity Molecular Discovery, Encoded Library Technologies, 830 Winter Street, Waltham, Massachusetts 02451, United States
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35
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Škopić MK, Salamon H, Bugain O, Jung K, Gohla A, Doetsch LJ, Dos Santos D, Bhat A, Wagner B, Brunschweiger A. Acid- and Au(i)-mediated synthesis of hexathymidine-DNA-heterocycle chimeras, an efficient entry to DNA-encoded libraries inspired by drug structures. Chem Sci 2017; 8:3356-3361. [PMID: 28507705 PMCID: PMC5416911 DOI: 10.1039/c7sc00455a] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/27/2017] [Indexed: 11/21/2022] Open
Abstract
Libraries of DNA-tagged compounds are a validated screening technology for drug discovery. They are synthesized through combinatorial iterations of alternated coding and preparative synthesis steps. Thus, large chemical space can be accessed for target-based screening. However, the need to preserve the functionality of the DNA tag severely restricts the choice of chemical methods for library synthesis. Acidic organocatalysts, transition metals, and oxidants furnish diverse drug-like structures from simple starting materials, but cause loss of genetic information by depurination. A hexathymidine oligonucleotide, called "hexT" allows the chemist utilizing these classes of catalysts to access a potentially broad variety of structures in the initial step of library synthesis. We exploited its catalyst tolerance to efficiently synthesize diverse substituted β-carbolines, pyrazolines, and pyrazoles from readily available starting materials as hexT conjugates by acid- and Au(i)-catalysis, respectively. The hexT conjugates were ligated to coding DNA sequences yielding encoded screening libraries inspired by drug structures.
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Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Hazem Salamon
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Olivia Bugain
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Kathrin Jung
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Anne Gohla
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Lara J Doetsch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Denise Dos Santos
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Avinash Bhat
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Bernd Wagner
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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36
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Thomas B, Lu X, Birmingham WR, Huang K, Both P, Reyes Martinez JE, Young RJ, Davie CP, Flitsch SL. Application of Biocatalysis to on-DNA Carbohydrate Library Synthesis. Chembiochem 2017; 18:858-863. [PMID: 28127867 DOI: 10.1002/cbic.201600678] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 01/14/2023]
Abstract
DNA-encoded libraries are increasingly used for the discovery of bioactive lead compounds in high-throughput screening programs against specific biological targets. Although a number of libraries are now available, they cover limited chemical space due to bias in ease of synthesis and the lack of chemical reactions that are compatible with DNA tagging. For example, compound libraries rarely contain complex biomolecules such as carbohydrates with high levels of functionality, stereochemistry, and hydrophilicity. By using biocatalysis in combination with chemical methods, we aimed to significantly expand chemical space and generate generic libraries with potentially better biocompatibility. For DNA-encoded libraries, biocatalysis is particularly advantageous, as it is highly selective and can be performed in aqueous environments, which is an essential feature for this split-and-mix library technology. In this work, we demonstrated the application of biocatalysis for the on-DNA synthesis of carbohydrate-based libraries by using enzymatic oxidation and glycosylation in combination with traditional organic chemistry.
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Affiliation(s)
- Baptiste Thomas
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Xiaojie Lu
- Encoded Library Technologies, NCE Molecular Discovery, R&D, Platform Technology & Science, GlaxoSmithKline, 830 Winter Street, Waltham, MA, 02451, USA
| | - William R Birmingham
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kun Huang
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Peter Both
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Juana Elizabeth Reyes Martinez
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Robert J Young
- Medicinal Chemistry, NCE Molecular Discovery, R&D, Platform Technology and Science, GlaxoSmithKline, GlaxoSmithKline Medicines Research Centre, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Christopher P Davie
- Encoded Library Technologies, NCE Molecular Discovery, R&D, Platform Technology & Science, GlaxoSmithKline, 830 Winter Street, Waltham, MA, 02451, USA
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology and, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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37
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Yuen LH, Franzini RM. Stability of Oligonucleotide-Small Molecule Conjugates to DNA-Deprotection Conditions. Bioconjug Chem 2017; 28:1076-1083. [PMID: 28233987 DOI: 10.1021/acs.bioconjchem.7b00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oligonucleotide conjugates of small molecules are widely used in chemical biology and have found increasing interest in the context of DNA-encoded chemical libraries for drug discovery. Attachment of molecules to DNA bound to the solid support is an attractive small-molecule conjugation method that permits the use of organic solvents, rigorous reaction conditions, and simple workup. However, the conjugated structures must be resistant to the harsh DNA deprotection/cleavage conditions and the stabilities of building blocks under various deprotection conditions are mostly unexplored. In the present study, we analyzed the stability of 131 structurally diverse fragments that contain amides and amide-like elements during DNA deprotection protocols. Structural features susceptible to decomposition in DNA deprotection conditions were identified and a protocol that enabled the synthesis of DNA conjugates with labile fragments on solid support was identified.
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Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
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38
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Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
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39
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Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
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40
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Ding Y, Franklin GJ, DeLorey JL, Centrella PA, Mataruse S, Clark MA, Skinner SR, Belyanskaya S. Design and Synthesis of Biaryl DNA-Encoded Libraries. ACS COMBINATORIAL SCIENCE 2016; 18:625-629. [PMID: 27571034 DOI: 10.1021/acscombsci.6b00078] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).
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Affiliation(s)
- Yun Ding
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - G. Joseph Franklin
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. DeLorey
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Matthew A. Clark
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Steven R. Skinner
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Svetlana Belyanskaya
- GlaxoSmithKline, Platform Technology & Science, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
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41
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Li Y, Gabriele E, Samain F, Favalli N, Sladojevich F, Scheuermann J, Neri D. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries. ACS COMBINATORIAL SCIENCE 2016; 18:438-43. [PMID: 27314981 DOI: 10.1021/acscombsci.6b00058] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
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Affiliation(s)
- Yizhou Li
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Elena Gabriele
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Nicholas Favalli
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | | | - Jörg Scheuermann
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
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42
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Zimmermann G, Neri D. DNA-encoded chemical libraries: foundations and applications in lead discovery. Drug Discov Today 2016; 21:1828-1834. [PMID: 27477486 DOI: 10.1016/j.drudis.2016.07.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/17/2016] [Accepted: 07/23/2016] [Indexed: 12/16/2022]
Abstract
DNA-encoded chemical libraries have emerged as a powerful tool for hit identification in the pharmaceutical industry and in academia. Similar to biological display techniques (such as phage display technology), DNA-encoded chemical libraries contain a link between the displayed chemical building block and an amplifiable genetic barcode on DNA. Using routine procedures, libraries containing millions to billions of compounds can be easily produced within a few weeks. The resulting compound libraries are screened in a single test tube against proteins of pharmaceutical interest and hits can be identified by PCR amplification of DNA barcodes and subsequent high-throughput sequencing.
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Affiliation(s)
- Gunther Zimmermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir Prelog Weg 1-5/10, CH-8093 Zürich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir Prelog Weg 1-5/10, CH-8093 Zürich, Switzerland.
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43
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Abstract
DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
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Affiliation(s)
- Marie L. Malone
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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Decurtins W, Wichert M, Franzini RM, Buller F, Stravs MA, Zhang Y, Neri D, Scheuermann J. Automated screening for small organic ligands using DNA-encoded chemical libraries. Nat Protoc 2016; 11:764-80. [PMID: 26985574 DOI: 10.1038/nprot.2016.039] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of organic compounds that are individually linked to different oligonucleotides, serving as amplifiable identification barcodes. As all compounds in the library can be identified by their DNA tags, they can be mixed and used in affinity-capture experiments on target proteins of interest. In this protocol, we describe the screening process that allows the identification of the few binding molecules within the multiplicity of library members. First, the automated affinity selection process physically isolates binding library members. Second, the DNA codes of the isolated binders are PCR-amplified and subjected to high-throughput DNA sequencing. Third, the obtained sequencing data are evaluated using a C++ program and the results are displayed using MATLAB software. The resulting selection fingerprints facilitate the discrimination of binding from nonbinding library members. The described procedures allow the identification of small organic ligands to biological targets from a DECL within 10 d.
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Affiliation(s)
- Willy Decurtins
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Moreno Wichert
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Raphael M Franzini
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Fabian Buller
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Michael A Stravs
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Yixin Zhang
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
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Affiliation(s)
- Raphael M. Franzini
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Cassie Randolph
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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46
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Salamon H, Klika Škopić M, Jung K, Bugain O, Brunschweiger A. Chemical Biology Probes from Advanced DNA-encoded Libraries. ACS Chem Biol 2016; 11:296-307. [PMID: 26820267 DOI: 10.1021/acschembio.5b00981] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.
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Affiliation(s)
- Hazem Salamon
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Mateja Klika Škopić
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Kathrin Jung
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Olivia Bugain
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
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47
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Škopić MK, Bugain O, Jung K, Onstein S, Brandherm S, Kalliokoski T, Brunschweiger A. Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00243a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-encoded libraries based on scaffolds functionalized for DNA-compatible chemistry were synthesized by split-and-pool combinatorial chemistry. The library design was aided by a chemoinformatic filtering cascade.
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Affiliation(s)
- M. Klika Škopić
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - O. Bugain
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - K. Jung
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Onstein
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Brandherm
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | | | - A. Brunschweiger
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
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48
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Novel PTP1B inhibitors identified by DNA display of fragment pairs. Bioorg Med Chem Lett 2015; 26:1080-1085. [PMID: 26691757 DOI: 10.1016/j.bmcl.2015.11.102] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 12/15/2022]
Abstract
DNA display of PNA-encoded libraries was used to pair fragments containing different phosphotyrosine surrogates with diverse triazoles. Microarray-based screening of the combinatorially paired fragment sets (62,500 combinations) against a prototypical phosphatase, PTP1B, was used to identify the fittest fragments. A focused library (10,000 members) covalently pairing identified fragments with linkers of different length and geometry was synthesized. Screening of the focused library against PTP1B and closely related TCPTP revealed orthogonal inhibitors. The selectivity of the identified inhibitors for PTP1B versus TCPT was confirmed by enzymatic inhibition assay.
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Franzini RM, Biendl S, Mikutis G, Samain F, Scheuermann J, Neri D. "Cap-and-Catch" Purification for Enhancing the Quality of Libraries of DNA Conjugates. ACS COMBINATORIAL SCIENCE 2015; 17:393-8. [PMID: 26083096 DOI: 10.1021/acscombsci.5b00072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential of DNA-encoded combinatorial libraries (DECLs) as tools for hit discovery crucially relies on the availability of methods for their synthesis at acceptable purity and quality. Incomplete reactions in the presence of DNA can noticeably affect the purity of DECLs and methods to selectively remove unreacted oligonucleotide-based starting products would likely enhance the quality of DECL screening results. We describe an approach to selectively remove unreacted oligonucleotide starting products from reaction mixtures and demonstrate its applicability in the context of acylation of amino-modified DNA. Following an amide bond forming reaction, we treat unreacted amino-modified DNAs with biotinylating reagents and isolate the corresponding biotinylated oligonucleotides from the reaction mixture by affinity capture on streptavidin-coated sepharose. This approach, which yields the desired DNA-conjugate at enhanced purity, can be applied both to reactions performed in solution and to procedures in which DNA is immobilized on an anion exchange solid support.
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Affiliation(s)
- Raphael M. Franzini
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Stefan Biendl
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | | | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Jörg Scheuermann
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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50
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Satz AL, Cai J, Chen Y, Goodnow R, Gruber F, Kowalczyk A, Petersen A, Naderi-Oboodi G, Orzechowski L, Strebel Q. DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries. Bioconjug Chem 2015; 26:1623-32. [DOI: 10.1021/acs.bioconjchem.5b00239] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Jianping Cai
- Roche Innovation Center, Basel 4070, Switzerland
| | - Yi Chen
- Hoffmann-La Roche, Inc., Nutley, New Jersey 07110, United States
| | - Robert Goodnow
- Hoffmann-La Roche, Inc., Nutley, New Jersey 07110, United States
| | - Felix Gruber
- Roche Innovation Center, Basel 4070, Switzerland
| | | | - Ann Petersen
- Roche Innovation Center, Basel 4070, Switzerland
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