1
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Fang X, Zhang T, Fang W, Zhang G, Li Y, Li Y. Synthesis of Functionalized Triazoles on DNA via Azide-Acetonitrile "Click" Reaction. Org Lett 2023; 25:8326-8331. [PMID: 37943666 DOI: 10.1021/acs.orglett.3c03404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Triazoles are privileged structural motifs that are embedded in a number of molecules with interesting biological activities. In this work, we developed a practical and general synthetic strategy to construct a medicinally important 5-amino-1,2,3-triazole moiety on DNA by coupling DNA-conjugated azides and monosubstituted acetonitriles via azide-acetonitrile "click" reaction. Under mild reaction conditions, this reaction displayed a broad substrate scope. Most substrates gave moderate-to-excellent conversions. Thus, this DNA-compatible reaction could be employed in practical DNA-encoded library (DEL) construction and potentially expand the chemical space of DNA-encoded libraries.
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Affiliation(s)
- Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, P. R. China
| | - Tianyang Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Wei Fang
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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2
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Mikami A, Mori S, Osawa T, Obika S. Post-Synthetic Nucleobase Modification of Oligodeoxynucleotides by Sonogashira Coupling and Influence of Alkynyl Modifications on the Duplex-Forming Ability. Chemistry 2023; 29:e202301928. [PMID: 37635089 DOI: 10.1002/chem.202301928] [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: 06/17/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Recently, it was reported that the alkynyl modification of nucleobases mitigates the toxicity of antisense oligonucleotides (ASO) while maintaining the efficacy. However, the general effect of alkynyl modifications on the duplex-forming ability of oligonucleotides (ONs) is unclear. In this study, post-synthetic nucleobase modification by Sonogashira coupling in aqueous medium was carried out to efficiently evaluate the physiological properties of various ONs with alkynyl-modified nucleobases. Although several undesired reactions, including nucleobase cyclization, were observed, various types of alkynyl-modified ONs were successfully obtained via Sonogashira coupling of ONs containing iodinated nucleobases. Evaluation of the stability of the duplex formed by the synthesized alkynyl-modified ONs showed that the alkynyl modification of pyrimidine was less tolerated than that of purine, although both the modifications occurred in the major groove of the duplex. These results can be attributed to the bond angle of the alkyne on the pyrimidine and the close proximity of the alkynyl substituents to the phosphodiester backbone. The synthetic method developed in this study may contribute to the screening of the optimal chemical modification of ASO because various alkynyl-modified ONs that are effective in reducing the toxicity of ASO can be easily synthesized by this method.
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Affiliation(s)
- Atsushi Mikami
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
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3
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Schneider L, Sauter B, Dagher K, Gillingham D. Recording Binding Information Directly into DNA-Encoded Libraries Using Terminal Deoxynucleotidyl Transferase. J Am Chem Soc 2023; 145:20874-20882. [PMID: 37704585 PMCID: PMC10540198 DOI: 10.1021/jacs.3c05961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 09/15/2023]
Abstract
Terminal deoxynucleotidyl transferase (TdT) is an unusual DNA polymerase that adds untemplated dNTPs to 3'-ends of DNA. If a target protein is expressed as a TdT fusion and incubated with a DNA-encoded library (DEL) in the presence of dATP, the binders of the target induce proximity between TdT and the DNA, promoting the synthesis of a poly-adenine (polyA) tail. The polyA tail length is proportional to the binding affinity, effectively serving as a stable molecular record of binding events. The polyA tail is also a convenient handle to enrich binders with magnetic poly(dT)25 beads before sequencing. In a benchmarking system, we show that ligands spanning nanomolar to double-digit micromolar binding can be cleanly identified by TdT extension, whereas only the tightest binding ligands are identified by classical affinity selection. The method is simple to implement and can function on any DEL that bears a free 3'-end.
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Affiliation(s)
| | - Basilius Sauter
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Koder Dagher
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University
of Basel, 4056 Basel, Switzerland
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4
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Merrifield JL, Pimentel EB, Peters-Clarke TM, Nesbitt DJ, Coon JJ, Martell JD. DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries. Bioconjug Chem 2023; 34:1380-1386. [PMID: 37540561 PMCID: PMC10831869 DOI: 10.1021/acs.bioconjchem.3c00254] [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] [Indexed: 08/06/2023]
Abstract
Aldehydes are important synthons for DNA-encoded library (DEL) construction, but the development of a DNA-compatible method for the oxidation of alcohols to aldehydes remains a significant challenge in the field of DEL chemistry. We report that a copper/TEMPO catalyst system enables the solution-phase DNA-compatible oxidation of DNA-linked primary activated alcohols to aldehydes. The semiaqueous, room-temperature reaction conditions afford oxidation of benzylic, heterobenzylic, and allylic alcohols in high yield, with DNA compatibility verified by mass spectrometry, qPCR, Sanger sequencing, and ligation assays. Subsequent transformations of the resulting aldehydes demonstrate the potential of this method for robust library diversification.
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Affiliation(s)
- Justice L. Merrifield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Daniel J. Nesbitt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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5
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Wang Y, Si X, Feng Y, Feng D, Xu X, Zhang Y. Ionizable Lipids with Triazole Moiety from Click Reaction for LNP-Based mRNA Delivery. Molecules 2023; 28:molecules28104046. [PMID: 37241787 DOI: 10.3390/molecules28104046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ionizable lipid-containing lipid nanoparticles (LNPs) as a non-viral vector with good safety and potency have been considered as an ideal delivery system for gene therapy. The screening of ionizable lipid libraries with common features but diverse structures holds the promise of finding new candidates for LNPs to deliver different nucleic acid drugs such as messenger RNAs (mRNAs). Chemical strategies for the facile construction of ionizable lipid libraries with diverse structure are in high demand. Here, we report on the ionizable lipids containing the triazole moiety prepared by the copper-catalyzed alkyne-azide click reaction (CuAAC). We demonstrated that these lipids served well as the major component of LNPs, in order to encapsulate mRNA using luciferase mRNA as the model system. Thus, this study shows the potential of click chemistry in the preparation of lipid libraries for LNP assembly and mRNA delivery.
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Affiliation(s)
- Yixiang Wang
- School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Advanced Organic Materials, State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiao Si
- School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Advanced Organic Materials, State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yi Feng
- School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Advanced Organic Materials, State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dan Feng
- Nanjing Vazyme Biotechnology Company, Nanjing 210034, China
| | - Xiaoyu Xu
- Nanjing Vazyme Biotechnology Company, Nanjing 210034, China
| | - Yan Zhang
- School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Advanced Organic Materials, State Key Laboratory of Analytical Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China
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6
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Luo A, Zhou H, Hua Q, An Y, Ma H, Zhao X, Yang K, Hu YJ. Development of the Inverse Sonogashira Reaction for DEL Synthesis. ACS Med Chem Lett 2023; 14:270-277. [PMID: 36923912 PMCID: PMC10009795 DOI: 10.1021/acsmedchemlett.2c00477] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
An efficient approach for aryl acetylene DNA-encoded library (DEL) synthesis was developed in this study by transition-metal-mediated inverse Sonogashira reaction of 1-iodoalkyne with boronic acid under ambient conditions, with moderate to excellent conversions and broad substrate adaptability for the first time. Compared to palladium-phosphine, copper iodide performed better in the on-DNA inverse Sonogashira reaction. Interestingly, substrate diversity can be enhanced by first interrogating coupling reagents under copper-promoted conditions, and then revalidating them under palladium-facilitated conditions for those reagents which failed under the former. This complementary validation strategy is particularly well-fitted to any DEL validation studies.
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Affiliation(s)
- Ayun Luo
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hongxia Zhou
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Qini Hua
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Yufang An
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Hangke Ma
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Xue Zhao
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
| | - Kexin Yang
- Pharmaron
Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, P. R. China
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7
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Stanway-Gordon H, Odger JA, Waring MJ. Development of a Micellar-Promoted Heck Reaction for the Synthesis of DNA-Encoded Libraries. Bioconjug Chem 2023; 34. [PMID: 36883323 PMCID: PMC10119937 DOI: 10.1021/acs.bioconjchem.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/22/2023] [Indexed: 03/09/2023]
Abstract
The capability of DNA encoded libraries (DELs) as a method of small molecule hit identification is becoming widely established in drug discovery. While their selection method offers advantages over more traditional means, DELs are limited by the chemistry that can be utilized to construct them. Significant advances in DNA compatible chemistry have been made over the past five years; however such procedures are still often burdened by substrate specificity and/or incomplete conversions, reducing the fidelity of the resulting libraries. One such reaction is the Heck coupling, for which current DNA-compatible protocols are somewhat unreliable. Utilizing micellar technology, we have developed a highly efficient DNA-compatible Heck reaction that proceeds on average to 95% conversion to product across a broad variety of structurally significant building blocks and multiple DNA conjugates. This work continues the application of micellar catalysis to the development of widely applicable, effective DNA-compatible reactions for use in DELs.
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Affiliation(s)
- Harriet
A. Stanway-Gordon
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
| | - Jake A. Odger
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
| | - Michael J. Waring
- Cancer Research Horizons
Therapeutic Innovation, Chemistry, School of Natural and Environmental
Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1
7RU, United Kingdom
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8
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Li X, Zhang J, Liu C, Sun J, Li Y, Zhang G, Li Y. Aryl diazonium intermediates enable mild DNA-compatible C-C bond formation for medicinally relevant combinatorial library synthesis. Chem Sci 2022; 13:13100-13109. [PMID: 36425486 PMCID: PMC9667928 DOI: 10.1039/d2sc04482j] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/24/2022] [Indexed: 08/24/2023] Open
Abstract
Forging carbon-carbon (C-C) linkage in DNA-encoded combinatorial library synthesis represents a fundamental task for drug discovery, especially with broad substrate scope and exquisite functional group tolerance. Here we reported the palladium-catalyzed Suzuki-Miyaura, Heck and Hiyama type cross-coupling via DNA-conjugated aryl diazonium intermediates for DNA-encoded chemical library (DEL) synthesis. Starting from commodity arylamines, this synthetic route facilely delivers vast chemical diversity at a mild temperature and pH, thus circumventing damage to fragile functional groups. Given its orthogonality with traditional aryl halide-based cross-coupling, the aryl diazonium-centered strategy expands the compatible synthesis of complex C-C bond-connected scaffolds. In addition, DNA-tethered pharmaceutical compounds (e.g., HDAC inhibitor) are constructed without decomposition of susceptible bioactive warheads (e.g., hydroxamic acid), emphasizing the superiority of the aryl diazonium-based approach. Together with the convenient transformation into an aryl azide photo-crosslinker, aryl diazonium's DNA-compatible diversification synergistically demonstrated its competence to create medicinally relevant combinatorial libraries and investigate protein-ligand interactions in pharmaceutical research.
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Affiliation(s)
- Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Changyang Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University P. R. China
- Beijing National Laboratory for Molecular Sciences Beijing 100190 P. R. China
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9
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Puglioli S, Schmidt E, Pellegrino C, Prati L, Oehler S, De Luca R, Galbiati A, Comacchio C, Nadal L, Scheuermann J, Manz MG, Neri D, Cazzamalli S, Bassi G, Favalli N. Selective tumor targeting enabled by picomolar fibroblast activation protein inhibitors isolated from a DNA-encoded affinity maturation library. Chem 2022. [DOI: 10.1016/j.chempr.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Dakhel S, Galbiati A, Migliorini F, Comacchio C, Oehler S, Prati L, Scheuermann J, Cazzamalli S, Neri D, Bassi G, Favalli N. Isolation of a Natural Killer Group 2D Small-Molecule Ligand from DNA-Encoded Chemical Libraries. ChemMedChem 2022; 17:e202200350. [PMID: 35929380 DOI: 10.1002/cmdc.202200350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/11/2022]
Abstract
Natural Killer Group 2D (NKG2D) is a homo-dimeric transmembrane protein which is typically expressed on the surface of natural killer (NK) cells, natural killer T (NKT) cells, gamma delta T (γδT) cells, activated CD8 positive T-cells and activated macrophages. Bispecific molecules, capable of bridging NKG2D with a target protein expressed on the surface of tumor cells, may be used to redirect the cytotoxic activity of NK-cells towards antigen-positive malignanT-cells. In this work, we report the discovery of a novel NKG2D small molecule binder [K D = (410±60) nM], isolated from a DNA-Encoded Chemical Library (DEL). The discovery of small organic NKG2D ligands may facilitate the generation of fully synthetic bispecific adaptors, which may serve as an alternative to bispecific antibody products and which may benefit from better tumor targeting properties.
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Affiliation(s)
| | | | | | | | | | - Luca Prati
- Philogen SpA, R&D (Philochem), SWITZERLAND
| | - Jörg Scheuermann
- ETH Zürich: Eidgenossische Technische Hochschule Zurich, chemistry and applied biosciences, SWITZERLAND
| | | | | | | | - Nicholas Favalli
- Philogen SpA, R&D (Philochem), Libernstrasse 3, 8112, Otelfingen, SWITZERLAND
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11
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Siripuram VK, Sunkari YK, Nguyen TL, Flajolet M. DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries. Front Chem 2022; 10:894603. [PMID: 35774858 PMCID: PMC9237475 DOI: 10.3389/fchem.2022.894603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
An efficient method for the C-C bond formation via water soluble Na2PdCl4/sSPhos mediated Suzuki-Miyaura cross-coupling reaction of DNA-conjugated aryl iodide with (het)aryl boronic acids has been developed. This reaction proceeds at 37°C in water and acetonitrile (4:1) system. We also demonstrated that numerous aromatic and heteroaromatic boronic acids of different electronic natures, and harboring various functional groups, were highly compatible providing the desired coupling products in good to excellent yields. This DNA-compatible Suzuki-Miyaura cross-coupling reaction has strong potential to construct DNA-Encoded Libraries (DELs) in the context of drug discovery.
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Affiliation(s)
| | | | | | - Marc Flajolet
- *Correspondence: Vijay Kumar Siripuram, ; Marc Flajolet,
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12
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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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13
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Krumb M, Kammer LM, Badir SO, Cabrera-Afonso MJ, Wu VE, Huang M, Csakai A, Marcaurelle LA, Molander GA. Photochemical C-H arylation of heteroarenes for DNA-encoded library synthesis. Chem Sci 2022; 13:1023-1029. [PMID: 35211268 PMCID: PMC8790789 DOI: 10.1039/d1sc05683b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/06/2021] [Indexed: 12/22/2022] Open
Abstract
DNA-encoded library (DEL) technology has emerged as a time- and cost-efficient technique for the identification of therapeutic candidates in the pharmaceutical industry. Although several reaction classes have been successfully validated in DEL environments, there remains a paucity of DNA-compatible reactions that harness building blocks (BBs) from readily available substructures bearing multifunctional handles for further library diversification under mild, dilute, and aqueous conditions. In this study, the direct C-H carbofunctionalization of medicinally-relevant heteroarenes can be accomplished via the photoreduction of DNA-conjugated (hetero)aryl halides to deliver reactive aryl radical intermediates in a regulated fashion within minutes of blue light illumination. A broad array of electron-rich and electron-poor heteroarene scaffolds undergo transformation in the presence of sensitive functional groups.
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Affiliation(s)
- Matthias Krumb
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Lisa Marie Kammer
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Shorouk O Badir
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - María Jesús Cabrera-Afonso
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Victoria E Wu
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Minxue Huang
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Adam Csakai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Lisa A Marcaurelle
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline 200 Cambridge Park Drive Cambridge MA 02140 USA
| | - Gary A Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
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14
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Plais L, Scheuermann J. Macrocyclic DNA-encoded chemical libraries: a historical perspective. RSC Chem Biol 2022; 3:7-17. [PMID: 35128404 PMCID: PMC8729180 DOI: 10.1039/d1cb00161b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
While macrocyclic peptides are extensively researched for therapeutically relevant protein targets, DNA-encoded chemical libraries (DELs) are developed at a quick pace to discover novel small molecule binders. The combination of both fields has been explored since 2004 and the number of macrocyclic peptide DELs is steadily increasing. Macrocycles with high affinity and potency were identified for diverse classes of proteins, revealing DEL's huge potential. By giving a historical perspective, we would like to review the methods which permitted the rise of macrocyclic peptide DELs, describe the different DELs which were created and discuss the achievements and challenges of this emerging field.
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Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
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15
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Scott SK. On-DNA-1,2,3-Triazole Formation via Click Reaction. Methods Mol Biol 2022; 2541:39-43. [PMID: 36083541 DOI: 10.1007/978-1-0716-2545-3_6] [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
Copper-catalyzed azide-alkyne cycloaddition (CuAAC) provides a simple and convenient strategy to synthesize diverse 1,2,3-triazoles for drug discovery. Described herein is a protocol for the CuSO4-catalyzed cycloaddition between alkynes and DNA-appended azides.
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Affiliation(s)
- Sarah K Scott
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
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16
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Hunter JH, Potowski M, Stanway-Gordon HA, Madin A, Pairaudeau G, Brunschweiger A, Waring MJ. Functional Group Tolerance of a Micellar on-DNA Suzuki-Miyaura Cross-Coupling Reaction for DNA-Encoded Library Design. J Org Chem 2021; 86:17930-17935. [PMID: 34816720 DOI: 10.1021/acs.joc.1c02259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA-encoded libraries (DELs) offer great promise for the discovery of new ligands for proteins. Many current reactions used for DEL synthesis do not proceed efficiently over a wide range of substrates. Combining a diverse array of multicomponent reactions with micellar-promoted Suzuki-Miyaura cross-coupling provides a strategy for synthesizing highly diverse DELs with exceptionally high fidelity. These results demonstrate that the micellar Suzuki-Miyaura reaction has exceptional functional group tolerance and broad applicability.
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Affiliation(s)
- James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Marco Potowski
- Research Group Medicinal Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Garry Pairaudeau
- Exscientia, Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Andreas Brunschweiger
- Research Group Medicinal Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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17
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Qi J, Liu S, Seydimemet M, Wang X, Lu X. A General Set of DNA-Compatible Reactions for Preparing DNA-Tagged Multisubstituted Pyrroles. Bioconjug Chem 2021; 32:2290-2294. [PMID: 34699185 DOI: 10.1021/acs.bioconjchem.1c00427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded library (DEL) technology provided a powerful screening platform for identifying potential bioactive small molecules with high affinity to biologically interesting targets. Essential to a successful DEL campaign are the drug-like small molecular moieties of DNA-encoded libraries with expanded chemical space. Our laboratory has been working on developing and producing novel DNA-encoded libraries that complement current reported DELs. Herein, we demonstrated a general set of DNA-compatible reactions that enable the preparation of pyrrole-based DNA-encoded libraries in which the DNA tags are linked to the N position of the pyrrole central core. Further diversification could be rapidly incorporated into the pyrrole scaffold by robust iodination and Suzuki coupling reactions.
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Affiliation(s)
- Jingjing Qi
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Mengnisa Seydimemet
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Xiaojie Lu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
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18
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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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19
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Favalli N, Bassi G, Pellegrino C, Millul J, De Luca R, Cazzamalli S, Yang S, Trenner A, Mozaffari NL, Myburgh R, Moroglu M, Conway SJ, Sartori AA, Manz MG, Lerner RA, Vogt PK, Scheuermann J, Neri D. Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications. Nat Chem 2021; 13:540-548. [PMID: 33833446 PMCID: PMC8405038 DOI: 10.1038/s41557-021-00660-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023]
Abstract
The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting.
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Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Christian Pellegrino
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Su Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA
| | - Peter K Vogt
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
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20
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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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21
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Yang P, Wang X, Li B, Yang Y, Yue J, Suo Y, Tong H, He G, Lu X, Chen G. Streamlined construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation in solution and on DNA. Chem Sci 2021; 12:5804-5810. [PMID: 34168804 PMCID: PMC8179660 DOI: 10.1039/d1sc00789k] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed. The method exhibits a broad substrate scope for thiols, aryl iodides and amino acid units. Peptide macrocycles of a wide range of size and composition can be readily assembled in high yield from various easily accessible building blocks. This method has been successfully employed to prepare an 8-million-membered tetrameric cyclic peptide DNA-encoded library (DEL). Preliminary screening of the DEL library against protein p300 identified compounds with single digit micromolar inhibition activity.
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Affiliation(s)
- Peng Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Yixuan Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Jinfeng Yue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Huarong Tong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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22
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Shi Y, Wu YR, Yu JQ, Zhang WN, Zhuang CL. DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output. RSC Adv 2021; 11:2359-2376. [PMID: 35424149 PMCID: PMC8693808 DOI: 10.1039/d0ra09889b] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
A DNA-encoded library is a collection of small molecules covalently linked to DNA that has unique information about the identity and the structure of each library member. A DNA-encoded chemical library (DEL) is broadly adopted by major pharmaceutical companies and used in numerous drug discovery programs. The application of the DEL technology is advantageous at the initial period of drug discovery because of reduced cost, time, and storage space for the identification of target compounds. The key points for the construction of DELs comprise the development and the selection of the encoding methods, transfer of routine chemical reaction from off-DNA to on-DNA, and exploration of new chemical reactions on DNA. The limitations in the chemical space and the diversity of DEL were reduced gradually by using novel DNA-compatible reactions based on the formation and the cleavage of various bonds. Here, we summarized a series of novel DNA-compatible chemistry reactions for DEL building blocks and analysed the druggability of screened hit molecules via DELs in the past five years.
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Affiliation(s)
- Ying Shi
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Yan-Ran Wu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Jian-Qiang Yu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Wan-Nian Zhang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| | - Chun-Lin Zhuang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
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23
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Priego J, de Pedro Beato E, Benavides J, Gironda-Martínez A, González F, Blas J, Martín-Ortega MD, Rama-Garda R, Ezquerra J, Toledo MA, Torrado A. On-DNA Palladium-Catalyzed Hydrogenation-like Reaction Suitable for DNA-Encoded Library Synthesis. Bioconjug Chem 2020; 32:88-93. [PMID: 33356163 DOI: 10.1021/acs.bioconjchem.0c00566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we describe a method to orthogonally remove on-DNA N-Cbz, N-Alloc, N-Allyl, O-Bn, and O-Allyl protecting groups in the presence of other common protecting groups to afford free amines and carboxylic acids, respectively. The developed method uses NaBH4 as the source of hydrogen in the presence of Pd(OAc)2 under DNA aqueous conditions. In addition, under the developed conditions we were able to successfully hydrogenate triple and double bonds to totally saturated compounds. Furthermore, we introduce a new alternative procedure to reduce azides and aromatic nitro compounds to primary amines.
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Affiliation(s)
- Julián Priego
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | - Jesús Benavides
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | - Fernando González
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Blas
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | | | - Ramón Rama-Garda
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Jesús Ezquerra
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Miguel A Toledo
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
| | - Alicia Torrado
- Centro de Investigación Lilly, S. A., 28108 Alcobendas, Madrid, Spain
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24
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Palladium-mediated Suzuki-Miyaura Cross-Coupling Reaction of Potassium Boc-protected aminomethyltrifluoroborate with DNA-Conjugated aryl bromides for DNA-Encoded chemical library synthesis. Biochem Biophys Res Commun 2020; 533:209-214. [DOI: 10.1016/j.bbrc.2020.04.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/05/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
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25
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Gao H, Lin S, Zhang S, Chen W, Liu X, Yang G, Lerner RA, Xu H, Zhou Z, Yi W. gem
‐Difluoromethylene Alkyne‐Enabled Diverse C−H Functionalization and Application to the on‐DNA Synthesis of Difluorinated Isocoumarins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hui Gao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Shuang Lin
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Weijie Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Xiawen Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
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26
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Gao H, Lin S, Zhang S, Chen W, Liu X, Yang G, Lerner RA, Xu H, Zhou Z, Yi W. gem
‐Difluoromethylene Alkyne‐Enabled Diverse C−H Functionalization and Application to the on‐DNA Synthesis of Difluorinated Isocoumarins. Angew Chem Int Ed Engl 2020; 60:1959-1966. [DOI: 10.1002/anie.202013052] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hui Gao
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Shuang Lin
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Weijie Chen
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Xiawen Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies & School of Life Science and Technology ShanghaiTech University Shanghai 201210 P. R. China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation & Molecular Target and Clinical Pharmacology the State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & the Fifth Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong 511436 P. R. China
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27
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Wen H, Ge R, Qu Y, Sun J, Shi X, Cui W, Yan H, Zhang Q, An Y, Su W, Yang H, Kuai L, Satz AL, Peng X. Synthesis of 1,2-Amino Alcohols by Photoredox-Mediated Decarboxylative Coupling of α-Amino Acids and DNA-Conjugated Carbonyls. Org Lett 2020; 22:9484-9489. [DOI: 10.1021/acs.orglett.0c03461] [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)
- Huanan Wen
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Rui Ge
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yi Qu
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jialin Sun
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hao Yan
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L. Satz
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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28
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Bassi G, Favalli N, Vuk M, Catalano M, Martinelli A, Trenner A, Porro A, Yang S, Tham CL, Moroglu M, Yue WW, Conway SJ, Vogt PK, Sartori AA, Scheuermann J, Neri D. A Single-Stranded DNA-Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001970. [PMID: 33240760 PMCID: PMC7675038 DOI: 10.1002/advs.202001970] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 06/11/2023]
Abstract
A versatile and Lipinski-compliant DNA-encoded library (DEL), comprising 366 600 glutamic acid derivatives coupled to oligonucleotides serving as amplifiable identification barcodes is designed, constructed, and characterized. The GB-DEL library, constructed in single-stranded DNA format, allows de novo identification of specific binders against several pharmaceutically relevant proteins. Moreover, hybridization of the single-stranded DEL with a set of known protein ligands of low to medium affinity coupled to a complementary DNA strand results in self-assembled selectable chemical structures, leading to the identification of affinity-matured compounds.
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Affiliation(s)
- Gabriele Bassi
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Miriam Vuk
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Adriano Martinelli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Anika Trenner
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Antonio Porro
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Su Yang
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | - Chuin Lean Tham
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Wyatt W. Yue
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Peter K. Vogt
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
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29
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Catalano M, Moroglu M, Balbi P, Mazzieri F, Clayton J, Andrews KH, Bigatti M, Scheuermann J, Conway SJ, Neri D. Selective Fragments for the CREBBP Bromodomain Identified from an Encoded Self-assembly Chemical Library. ChemMedChem 2020; 15:1752-1756. [PMID: 32686307 DOI: 10.1002/cmdc.202000528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/21/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i. e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i. e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore encoded self-assembly chemical (ESAC) library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from library selection showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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Affiliation(s)
- Marco Catalano
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Petra Balbi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Federica Mazzieri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - James Clayton
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katrina H Andrews
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Stuart J Conway
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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30
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Wen X, Duan Z, Liu J, Lu W, Lu X. On-DNA Cross-Dehydrogenative Coupling Reaction toward the Synthesis of Focused DNA-Encoded Tetrahydroisoquinoline Libraries. Org Lett 2020; 22:5721-5725. [DOI: 10.1021/acs.orglett.0c01565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Jiaxiang Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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31
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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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32
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Götte K, Chines S, Brunschweiger A. Reaction development for DNA-encoded library technology: From evolution to revolution? Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151889] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Xu H, Gu Y, Zhang S, Xiong H, Ma F, Lu F, Ji Q, Liu L, Ma P, Hou W, Yang G, Lerner RA. A Chemistry for Incorporation of Selenium into DNA‐Encoded Libraries. Angew Chem Int Ed Engl 2020; 59:13273-13280. [DOI: 10.1002/anie.202003595] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Wei Hou
- College of Pharmaceutical Science Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
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34
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Xu H, Gu Y, Zhang S, Xiong H, Ma F, Lu F, Ji Q, Liu L, Ma P, Hou W, Yang G, Lerner RA. A Chemistry for Incorporation of Selenium into DNA‐Encoded Libraries. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
- School of Life Science and Technology ShanghaiTech University 201210 Shanghai China
- Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Wei Hou
- College of Pharmaceutical Science Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University 201210 Shanghai China
| | - Richard A. Lerner
- Department of Chemistry Scripps Research Institute La Jolla CA 92037 USA
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35
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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36
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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: 99] [Impact Index Per Article: 24.8] [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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37
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Hunter JH, Prendergast L, Valente LF, Madin A, Pairaudeau G, Waring MJ. High Fidelity Suzuki-Miyaura Coupling for the Synthesis of DNA Encoded Libraries Enabled by Micelle Forming Surfactants. Bioconjug Chem 2020; 31:149-155. [PMID: 31873005 DOI: 10.1021/acs.bioconjchem.9b00838] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA encoded chemical libraries provide a highly efficient means of screening vast numbers of small molecules against an immobilized protein target. Their potential is currently restricted by the constraints of carrying out library synthesis in the presence of attached DNA tags, for which a limited number of reactions and substrates can be used. Even established reactions, such as Suzuki-Miyaura couplings, do not give efficient coupling reactions across a wide range of substrates and can lead to significant DNA degradation. We developed an efficient protocol for carrying out Suzuki-Miyaura couplings on DNA tagged substrates that proceeds with unprecedented efficiency to the desired biaryl products (>98% on average with no detectable DNA degradation) across a wide range of drug-like substrates using a micellar promoted process with commercial TPGS-750-M surfactant. We have demonstrated the applicability of this method in DEL synthesis by preparing a prototypical two-dimensional 36-member library employing the Suzuki-Miyaura coupling methodology as the final library synthesis step. This work shows, for the first time, that standard micellar surfactants can promote reactions for encoded library synthesis, leading to libraries of exceptional fidelity, and demonstrates the potential to expand the range of accessible DNA compatible chemistry.
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Affiliation(s)
- James H Hunter
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
| | - Lisa Prendergast
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer , Newcastle University , Paul O'Gorman Building, Framlington Place , Newcastle upon Tyne NE2 4AD , U.K
| | - Louis F Valente
- JMP Division , SAS Institute Inc. , 100 SAS Campus Drive , Cary , North Carolina 27513 , United States
| | - Andrew Madin
- Discovery Sciences IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K
| | - Garry Pairaudeau
- Discovery Sciences IMED Biotech Unit , AstraZeneca , 310 Cambridge Science Park, Milton Road , Cambridge CB4 0WG , U.K
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences , Newcastle University , Bedson Building , Newcastle upon Tyne NE1 7RU , U.K
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38
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Xu H, Ma F, Wang N, Hou W, Xiong H, Lu F, Li J, Wang S, Ma P, Yang G, Lerner RA. DNA-Encoded Libraries: Aryl Fluorosulfonates as Versatile Electrophiles Enabling Facile On-DNA Suzuki, Sonogashira, and Buchwald Reactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1901551. [PMID: 31832315 PMCID: PMC6891896 DOI: 10.1002/advs.201901551] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/04/2019] [Indexed: 05/07/2023]
Abstract
Using (hetero)aryl fluorosulfonates as versatile electrophiles, facile on-DNA cross-coupling reactions of Suzuki, Sonogashira, and Buchwald are reported here. Notably, all of these reactions show excellent functional group tolerance, mild reaction conditions (relative low temperature and open to air), rich heterocyclic coupling partners, and more importantly, DNA-compatibility. Thus, these new reactions based on efficient formation of C(sp2)-C(sp2), C(sp2)-C(sp), and C(sp2)-N bonds are highly amenable to synthesis of DNA-encoded libraries with great molecular diversity.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Nan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Wei Hou
- College of Pharmaceutical Scienceand Institute of Drug Development & Chemical Biology (IDD & CB)Zhejiang University of TechnologyHangzhou310014China
| | - Huan Xiong
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Fengping Lu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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39
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Gironda-Martínez A, Neri D, Samain F, Donckele EJ. DNA-Compatible Diazo-Transfer Reaction in Aqueous Media Suitable for DNA-Encoded Chemical Library Synthesis. Org Lett 2019; 21:9555-9558. [DOI: 10.1021/acs.orglett.9b03726] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Dario Neri
- 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, CH-8112 Otelfingen, Switzerland
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40
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Ratnayake AS, Flanagan ME, Foley TL, Smith JD, Johnson JG, Bellenger J, Montgomery JI, Paegel BM. A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis. ACS COMBINATORIAL SCIENCE 2019; 21:650-655. [PMID: 31425646 PMCID: PMC6938256 DOI: 10.1021/acscombsci.9b00113] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA-encoded chemical library (DECL) synthesis must occur in aqueous media under conditions that preserve the integrity of the DNA encoding tag. While the identification of "DNA-compatible" reaction conditions is critical for the development of DECL designs that explore previously inaccessible chemical space, reports measuring such compatibility have been largely restricted to methods that do not faithfully capture the impact of reaction conditions on DNA fidelity in solution phase. Here we report a comprehensive methodology that uses soluble DNA substrates that exactly recapitulate DNA's exposure to the chemically reactive species of DECL synthesis. This approach includes the assessment of chemical fidelity (reaction yield and purity), encoding fidelity (ligation efficiency), and readability (DNA compatibility), revealing the fate of the DNA tag during DECL chemistry from a single platform.
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Affiliation(s)
- Anokha S. Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Timothy L. Foley
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin D. Smith
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jillian G. Johnson
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin I. Montgomery
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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41
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Kölmel DK, Meng J, Tsai MH, Que J, Loach RP, Knauber T, Wan J, Flanagan ME. On-DNA Decarboxylative Arylation: Merging Photoredox with Nickel Catalysis in Water. ACS COMBINATORIAL SCIENCE 2019; 21:588-597. [PMID: 31283168 DOI: 10.1021/acscombsci.9b00076] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new catalytic manifold that merges photoredox with nickel catalysis in aqueous solution is presented. Specifically, the combination of a highly active, yet air-stable, nickel precatalyst with a new electron-deficient pyridyl carboxamidine ligand was key to the development of a water-compatible nickel catalysis platform, which is a crucial requirement for the preparation of DNA-encoded libraries (DELs). Together with an iridium-based photocatalyst and a powerful light source, this dual catalysis approach enabled the efficient decarboxylative arylation of α-amino acids with DNA-tagged aryl halides. This C(sp2)-C(sp3) coupling tolerates a wide variety of functional groups on both the amino acid and the aryl halide substrates. Due to the mild and DNA-compatible reaction conditions, the presented transformation holds great potential for the construction of DELs. This was further evidenced by showing that well plate-compatible LED arrays can serve as competent light sources to facilitate parallel synthesis. Lastly, we demonstrate that this procedure can serve as a blueprint toward the adaptation of other established nickel metallaphotoredox transformations to the idiosyncratic requirements of a DEL.
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Affiliation(s)
- Dominik K. Kölmel
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jiang Meng
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Mei-Hsuan Tsai
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Jiamin Que
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Richard P. Loach
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Thomas Knauber
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jinqiao Wan
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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