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Zhao G, Zhu M, Li Y, Zhang G, Li Y. Using DNA-encoded libraries of fragments for hit discovery of challenging therapeutic targets. Expert Opin Drug Discov 2024; 19:725-740. [PMID: 38753553 DOI: 10.1080/17460441.2024.2354287] [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] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION The effectiveness of Fragment-based drug design (FBDD) for targeting challenging therapeutic targets has been hindered by two factors: the small library size and the complexity of the fragment-to-hit optimization process. The DNA-encoded library (DEL) technology offers a compelling and robust high-throughput selection approach to potentially address these limitations. AREA COVERED In this review, the authors propose the viewpoint that the DEL technology matches perfectly with the concept of FBDD to facilitate hit discovery. They begin by analyzing the technical limitations of FBDD from a medicinal chemistry perspective and explain why DEL may offer potential solutions to these limitations. Subsequently, they elaborate in detail on how the integration of DEL with FBDD works. In addition, they present case studies involving both de novo hit discovery and full ligand discovery, especially for challenging therapeutic targets harboring broad drug-target interfaces. EXPERT OPINION The future of DEL-based fragment discovery may be promoted by both technical advances and application scopes. From the technical aspect, expanding the chemical diversity of DEL will be essential to achieve success in fragment-based drug discovery. From the application scope side, DEL-based fragment discovery holds promise for tackling a series of challenging targets.
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Affiliation(s)
- Guixian Zhao
- Chongqing University FuLing Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Mengping Zhu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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2
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Anderson MJ, Carton TP, Salvini CLA, Crawford JJ, Pairaudeau G, Waring MJ. Micelle-Promoted Reductive Amination of DNA-Conjugated Amines for DNA-Encoded Library Synthesis. Chemistry 2024; 30:e202400239. [PMID: 38251309 DOI: 10.1002/chem.202400239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/23/2024]
Abstract
DNA-encoded libraries (DELs) have become a leading technology for hit identification in drug discovery projects as large, diverse libraries can be generated. DELs are commonly synthesised via split-and-pool methodology; thus, chemical transformations utilised must be highly efficient, proceeding with high conversions. Reactions performed in DEL synthesis also require a broad substrate scope to produce diverse, drug-like libraries. Many pharmaceutical compounds incorporate multiple C-N bonds, over a quarter of which are synthesised via reductive aminations. However, few on-DNA reductive amination procedures have been developed. Herein is reported the application of the micelle-forming surfactant, TPGS-750-M, to the on-DNA reductive amination of DNA-conjugated amines, yielding highly efficient conversions with a broad range of aldehydes, including medicinally relevant heterocyclic and aliphatic substrates. The procedure is compatible with DNA amplification and sequencing, demonstrating its applicability to DEL synthesis.
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Affiliation(s)
- Matthew J Anderson
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Thomas P Carton
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
| | | | | | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne, NE1 7RU, UK
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3
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Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
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Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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4
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Zhang J, Liu J, Li X, Ju Y, Li Y, Zhang G, Li Y. Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine. J Am Chem Soc 2024; 146:2122-2131. [PMID: 38190443 DOI: 10.1021/jacs.3c11574] [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: 01/10/2024]
Abstract
Bioconjugation chemistry has emerged as a powerful tool for the modification of diverse biomolecules under mild conditions. Tetrazole, initially proposed as a bioorthogonal photoclick handle for 1,3-dipolar cyclization with alkenes, was later demonstrated to possess broader photoreactivity with carboxylic acids, serving as a versatile bioconjugation and photoaffinity labeling probe. In this study, we unexpectedly discovered and validated the photoreactivity between tetrazole and primary amine to afford a new 1,2,4-triazole cyclization product. Given the significance of functionalized N-heterocycles in medicinal chemistry, we successfully harnessed the serendipitously discovered reaction to synthesize both pharmacologically relevant DNA-encoded chemical libraries (DELs) and small molecule compounds bearing 1,2,4-triazole scaffolds. Furthermore, the mild reaction conditions and stable 1,2,4-triazole linkage found broad application in photoinduced bioconjugation scenarios, spanning from intramolecular peptide macrocyclization and templated DNA reaction cross-linking to intermolecular photoaffinity labeling of proteins. Triazole cross-linking products on lysine side chains were identified in tetrazole-labeled proteins, refining the comprehensive understanding of the photo-cross-linking profiles of tetrazole-based probes. Altogether, this tetrazole-amine bioconjugation expands the current bioconjugation toolbox and creates new possibilities at the interface of medicinal chemistry and chemical biology.
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Affiliation(s)
- Juan 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
| | - Jinlu Liu
- 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
| | - Xianfeng 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
| | - Yunzhu Ju
- 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
| | - 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
| | - 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
| | - 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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5
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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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6
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Zhang P, Koch G, Zhang Y, Yang K, Lokey RS. DNA-Compatible Conditions for the Formation of N-Methyl Peptide Bonds. ACS OMEGA 2023; 8:23477-23483. [PMID: 37426286 PMCID: PMC10323948 DOI: 10.1021/acsomega.3c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023]
Abstract
DNA-encoded libraries (DELs) are a powerful platform in drug discovery. Peptides have unique properties that make them attractive pharmaceutical candidates. N-methylation of the peptide backbone can confer beneficial properties such as increased proteolytic stability and membrane permeability. Herein, we evaluate different DEL reaction systems and report a DNA-compatible protocol for forming N-methylated amide bonds. The DNA-compatible, bis(trichloromethyl)carbonate-mediated amide coupling is efficient for the formation of N-methyl peptide bonds, which promises to increase the opportunity to identify passively cell-permeable macrocyclic peptide hits by DNA-encoded technology.
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Affiliation(s)
- Panpan Zhang
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Grant Koch
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - Yankun Zhang
- College
of Letters and Science, University of California
Santa Barbara, Santa
Barbara, California 93106, United States
| | - Kevin Yang
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California Santa Cruz, Santa
Cruz, California 95064, United States
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7
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An Y, Lee J, Seo H, Bae S, Kang J, Lee J, Kim J, Nam MH, Song M, Hwang GT. Groebke-Blackburn-Bienaymé Reaction for DNA-Encoded Library Technology. Org Lett 2023; 25:4445-4450. [PMID: 37310879 DOI: 10.1021/acs.orglett.3c01366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study presents a DNA-compatible synthesis of diverse 5-arylimidazo[1,2-a]pyridin-3-amine derivatives using the Suzuki-Miyaura reaction, followed by a Groebke-Blackburn-Bienaymé (GBB) reaction. The GBB reaction demonstrates a wide substrate scope, mild one-pot reaction conditions, and compatibility with subsequent enzymatic ligation, highlighting its potential in DNA-encoded library technology.
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Affiliation(s)
- Yujin An
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Juyeon Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyewon Seo
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Seri Bae
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jihee Kang
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jieon Lee
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Jinwoo Kim
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Myung Hee Nam
- Seoul Center, Korea Basic Science Institute (KBSI), Seoul 02841, Republic of Korea
| | - Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDIhub), Daegu 41061, Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Republic of Korea
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8
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Nan J, Huang G, Liu S, Wang J, Ma Y, Luan X. In(OTf) 3-catalyzed reorganization/cycloaddition of two imine units and subsequent modular assembly of acridinium photocatalysts. Chem Sci 2023; 14:5160-5166. [PMID: 37206409 PMCID: PMC10189902 DOI: 10.1039/d3sc00163f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/15/2023] [Indexed: 05/21/2023] Open
Abstract
Herein, we disclose a novel reorganization/cycloaddition between two imine units catalyzed by In(OTf)3 Lewis acid that differs from the well-known [4 + 2] cycloaddition version via the Povarov reaction. By means of this unprecedented imine chemistry, a collection of synthetically useful dihydroacridines has been synthesized. Notably, the obtained products give rise to a series of structurally novel and fine-tuneable acridinium photocatalysts, offering a heuristic paradigm for synthesis and efficiently facilitating several encouraging dihydrogen coupling reactions.
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Affiliation(s)
- Jiang Nan
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Guanjie Huang
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Shilei Liu
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Jing Wang
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Yangmin Ma
- The Youth Innovation Team of Shaanxi Universities, Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology Xi'an 710021 China
| | - Xinjun Luan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University Xi'an 710021 China
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Xu H, Tan T, Zhang Y, Wang Y, Pan K, Yao Y, Zhang S, Gu Y, Chen W, Li J, Dong H, Meng Y, Ma P, Hou W, Yang G. Metal-Free and Open-Air Arylation Reactions of Diaryliodonium Salts for DNA-Encoded Library Synthesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202790. [PMID: 35853237 PMCID: PMC9475524 DOI: 10.1002/advs.202202790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
A successful DNA-encoded library (DEL) will consist of diverse skeletons and cover chemical space as comprehensive as possible to fully realize its potential in drug discovery and chemical biology. However, the lack of versatile on-DNA arylation methods for phenols that are less nucleophilic and reactive poses a great hurdle for DEL to include diaryl ether, a privileged chemotype in pharmaceuticals and natural products. This work describes the use of "substrate activation" approach to address the arylation of DNA-conjugated phenols. Diaryliodonium salt, a highly electrophilic and reactive arylation reagent, is employed as Ar+ sources to ensure highly selective on-DNA arylation of phenols and oximes with both high yields and DNA fidelity. Notably, the new on-DNA arylation reaction can be applied to the late-stage modification of peptides containing tyrosine side-chain and to synthesize DNA-tagged analogues of existing drug molecules such as sorafenib, a known pan-kinase inhibitor. The new on-DNA diaryliodonium salts chemistry affords a greater flexibility in DEL design and synthesis.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Kangyin Pan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Ying Yao
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Yu Meng
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
- Shanghai Key Laboratory of Orthopedic ImplantsDepartment of Orthopedic SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong UniversitySchool of MedicineShanghai200011P. R. China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
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10
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Tang C, McInnes BT. Cascade Processes with Micellar Reaction Media: Recent Advances and Future Directions. Molecules 2022; 27:molecules27175611. [PMID: 36080376 PMCID: PMC9458028 DOI: 10.3390/molecules27175611] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/26/2022] Open
Abstract
Reducing the use of solvents is an important aim of green chemistry. Using micelles self-assembled from amphiphilic molecules dispersed in water (considered a green solvent) has facilitated reactions of organic compounds. When performing reactions in micelles, the hydrophobic effect can considerably accelerate apparent reaction rates, as well as enhance selectivity. Here, we review micellar reaction media and their potential role in sustainable chemical production. The focus of this review is applications of engineered amphiphilic systems for reactions (surface-active ionic liquids, designer surfactants, and block copolymers) as reaction media. Micelles are a versatile platform for performing a large array of organic chemistries using water as the bulk solvent. Building on this foundation, synthetic sequences combining several reaction steps in one pot have been developed. Telescoping multiple reactions can reduce solvent waste by limiting the volume of solvents, as well as eliminating purification processes. Thus, in particular, we review recent advances in “one-pot” multistep reactions achieved using micellar reaction media with potential applications in medicinal chemistry and agrochemistry. Photocatalyzed reactions in micellar reaction media are also discussed. In addition to the use of micelles, we emphasize the process (steps to isolate the product and reuse the catalyst).
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Affiliation(s)
- Christina Tang
- Chemical and Life Science Engineering Department, Virginia Commonwealth University, Richmond, VA 23284, USA
- Correspondence:
| | - Bridget T. McInnes
- Computer Science Department, Virginia Commonwealth University, Richmond, VA 23284, USA
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11
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Xu H, Wang Y, Dong H, Zhang Y, Gu Y, Zhang S, Meng Y, Li J, Shi XJ, Ji Q, Liu L, Ma P, Ma F, Yang G, Hou W. Selenylation Chemistry Suitable for On‐Plate Parallel and On‐DNA Library Synthesis Enabling High‐Throughput Medicinal Chemistry. Angew Chem Int Ed Engl 2022; 61:e202206516. [DOI: 10.1002/anie.202206516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yu Meng
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Xiao Jie Shi
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
- Shanghai Key Laboratory of Orthopedic Implants Department of Orthopedic Surgery Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine 201210 Shanghai China
- Zhejiang Laboratory Hangzhou 311121 China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
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12
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Choudhary D, Garg S, Kaur M, Sohal HS, Malhi DS, Kaur L, Verma M, Sharma A, Mutreja V. Advances in the Synthesis and Bio-Applications of Pyrazine Derivatives: A Review. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2092873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Dimple Choudhary
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Sonali Garg
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Manvinder Kaur
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Harvinder Singh Sohal
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Dharambeer Singh Malhi
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Loveleen Kaur
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Meenakshi Verma
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Ajay Sharma
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
| | - Vishal Mutreja
- Medicinal and Natural Product Laboratory, Department of Chemistry, Chandigarh University, Mohali, India
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13
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Petersen H, Ballmann M, Krause N, Weberskirch R. Gold(I) NHC Catalysts Immobilized to Amphiphilic Block Copolymers: A Versatile Approach to Micellar Gold Catalysis in Water. ChemCatChem 2022. [DOI: 10.1002/cctc.202200727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hanne Petersen
- TU Dortmund University: Technische Universitat Dortmund Fakultät für Chemie und Chem. Biologie Otto-Hahn Str. 6 44227 Dortmund GERMANY
| | - Monika Ballmann
- Technische Universität Dortmund: Technische Universitat Dortmund Fakultät für Chemie und Chem. Biologie Otto-Hahn Str. 6 44227 Dortmund GERMANY
| | - Norbert Krause
- TU Dortmund University: Technische Universitat Dortmund Fakultät für Chemie und Chem. Biologie Otto-Hahn Str. 6 44227 Dortmund GERMANY
| | - Ralf Weberskirch
- Dortmund University of Technology Fakultät Chemie und Chem. Biologie , organic chemistry Otto-Hahn-Str. 6Room: C2-04-702 44227 Dortmund GERMANY
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14
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Xu H, Wang Y, Dong H, Zhang Y, Gu Y, Zhang S, Meng Y, Li J, Shi XJ, Ji Q, Liu L, Ma P, Ma F, Yang G, Hou W. Selenylation Chemistry Suitable for On‐Plate Parallel and On‐DNA Library Synthesis Enabling High‐Throughput Medicinal Chemistry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Yu Meng
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Xiao Jie Shi
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Qun Ji
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
- Shanghai Key Laboratory of Orthopedic Implants Department of Orthopedic Surgery Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine 201210 Shanghai China
- Zhejiang Laboratory Hangzhou 311121 China
| | - Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech University Shanghai 201210 China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology Zhejiang University of Technology Hangzhou 310014 China
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15
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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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16
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de Fátima Â, Fernandes SA, Ferreira de Paiva W, de Freitas Rego Y. The Povarov Reaction: A Versatile Method to Synthesize Tetrahydroquinolines, Quinolines and Julolidines. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1794-8355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractThe multicomponent Povarov reaction represents a powerful approach for the construction of substances containing N-heterocyclic frameworks. By using the Povarov reaction, in addition to accessing tetrahydroquinolines, quinolines and julolidines in a single step, it is possible to form the following new bonds: two Csp
3–Csp
3 and one Csp
3–Nsp
3, two Csp
2–Csp
2 and one Csp
2–Nsp
2, and four Csp
3–Csp
3 and two Csp
3–Nsp
1, respectively. This short review discusses the main features of the Povarov reaction, including its mechanism, the reaction scope by employing different catalysts and substrates, as well as stereoselective versions.1 Introduction2 Mechanism of the Povarov Reaction3 Tetrahydroquinolines4 Quinolines5 Julolidines6 Concluding Remarks
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Affiliation(s)
- Ângelo de Fátima
- Departamento de Química, ICEx, Universidade Federal de Minas Gerais
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17
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Azhdari A, Azizi N, Sanaeishoar H, Tahanpesar E. Sb(III)-Impregnated Magnetic Carbon Nitride Nanosheets: Preparation, Characterization, and Evaluation of Its Catalytic Activity for Synthesis of Imidazo-Pyridines. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2036776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Asieh Azhdari
- Department of Chemistry, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran
| | - Najmedin Azizi
- Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Haleh Sanaeishoar
- Department of Chemistry, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran
| | - Elham Tahanpesar
- Department of Chemistry, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran
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18
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Huang Y, Li Y, Li X. Strategies for developing DNA-encoded libraries beyond binding assays. Nat Chem 2022; 14:129-140. [PMID: 35121833 DOI: 10.1038/s41557-021-00877-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries (DELs) have emerged as a powerful technology in drug discovery. The wide adoption of DELs in the pharmaceutical industry and the rapid advancements of DEL-compatible chemistry have further fuelled its development and applications. In general, a DEL has been considered as a massive binding assay to identify physical binders for individual protein targets. However, recent innovations demonstrate the capability of DELs to operate in the complex milieu of biological systems. In this Perspective, we discuss the recent progress in using DNA-encoded chemical libraries to interrogate complex biological targets and their potential to identify structures that elicit function or possess other useful properties. Future breakthroughs in these aspects are expected to catapult DEL to become a momentous technology platform not only for drug discovery but also to explore fundamental biology.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Hong Kong SAR, China.
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19
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for expanding encoded chemical diversification and improving hit enrichment in mRNA-displayed peptide libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA‐encoded small‐molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide‐tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the ‘drug‐likeness’ of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA‐encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA‐encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA‐displayed peptide library to allow a more diversity‐oriented approach to library modification. Finally, we outline alternate approaches for enriching target‐binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA‐display based approach could be used to discover new ‘drug‐like’ modified small peptides.
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Affiliation(s)
- Paddy R A Melsen
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Ryoji Yoshisada
- Vrije Universiteit Amsterdam, Department of Chemistry and Pharmaceutical Sciences, NETHERLANDS
| | - Seino A K Jongkees
- Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, de Boelelaan 1108, 1081 HZ, Amsterdam, NETHERLANDS
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20
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Coban D, Gridina O, Karg M, Gröschel AH. Morphology Control of Multicompartment Micelles in Water through Hierarchical Self-Assembly of Amphiphilic Terpolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deniz Coban
- Institute of Physical Chemistry, Center for Soft Nanoscience (SoN), and Center for Nanotechnology (CeNTech), University of Münster, 48149 Münster, Germany
| | - Olga Gridina
- Colloids and Nanooptics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Matthias Karg
- Colloids and Nanooptics, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - André H. Gröschel
- Institute of Physical Chemistry, Center for Soft Nanoscience (SoN), and Center for Nanotechnology (CeNTech), University of Münster, 48149 Münster, Germany
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21
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Stanway‐Gordon HA, Graham JS, Waring MJ. On-DNA Transfer Hydrogenolysis and Hydrogenation for the Synthesis of DNA-Encoded Chemical Libraries. Angew Chem Int Ed Engl 2022; 61:e202111927. [PMID: 34748693 PMCID: PMC9298793 DOI: 10.1002/anie.202111927] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 01/13/2023]
Abstract
DNA-encoded libraries (DELs) are an increasingly popular approach to finding small molecule ligands for proteins. Many DEL synthesis protocols hinge on sequential additions of monomers using split-pool combinatorial methods. Therefore, compatible protecting group strategies that allow the unmasking of reactive functionality (e. g. amines and alcohols) prior to monomer coupling, or the removal of less desirable functionality (e. g., alkenes and alkynes) are highly desirable. Hydrogenation/hydrogenolysis procedures would achieve these ends but have not been amenable to DEL chemistry. We report a catalytic hydrogen transfer reaction using Pd/C, HCONH4 and the micelle-forming surfactant, TPGS-750-M, which gives highly efficient conversions for hydrogenolysis of Cbz-protected amines and benzyl protected alcohols and hydrogenation of nitros, halides, nitriles, aldehydes, alkenes and alkynes. Application to multicycle synthesis of an encoded compound was fully compatible with DNA-amplification and sequencing, demonstrating its applicability to DEL synthesis. This method will enable synthetic DEL sequences using orthogonal protecting groups.
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Affiliation(s)
- Harriet A. Stanway‐Gordon
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
| | - Jessica S. Graham
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
| | - Michael J. Waring
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
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22
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Stanway‐Gordon HA, Graham JS, Waring MJ. On-DNA Transfer Hydrogenolysis and Hydrogenation for the Synthesis of DNA-Encoded Chemical Libraries. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202111927. [PMID: 38505343 PMCID: PMC10946939 DOI: 10.1002/ange.202111927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Indexed: 11/08/2022]
Abstract
DNA-encoded libraries (DELs) are an increasingly popular approach to finding small molecule ligands for proteins. Many DEL synthesis protocols hinge on sequential additions of monomers using split-pool combinatorial methods. Therefore, compatible protecting group strategies that allow the unmasking of reactive functionality (e. g. amines and alcohols) prior to monomer coupling, or the removal of less desirable functionality (e. g., alkenes and alkynes) are highly desirable. Hydrogenation/hydrogenolysis procedures would achieve these ends but have not been amenable to DEL chemistry. We report a catalytic hydrogen transfer reaction using Pd/C, HCONH4 and the micelle-forming surfactant, TPGS-750-M, which gives highly efficient conversions for hydrogenolysis of Cbz-protected amines and benzyl protected alcohols and hydrogenation of nitros, halides, nitriles, aldehydes, alkenes and alkynes. Application to multicycle synthesis of an encoded compound was fully compatible with DNA-amplification and sequencing, demonstrating its applicability to DEL synthesis. This method will enable synthetic DEL sequences using orthogonal protecting groups.
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Affiliation(s)
- Harriet A. Stanway‐Gordon
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
| | - Jessica S. Graham
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
| | - Michael J. Waring
- Cancer Research UK Newcastle Drug Discovery UnitChemistrySchool of Natural and Environmental SciencesNewcastle UniversityBedson BuildingNewcastle upon TyneNE1 7RUUK
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23
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Hosseini A, Motavalizadehkakhky A, Ghobadi N, Gholamzadeh P. Aza-Diels-Alder reactions in the synthesis of tetrahydroquinoline structures. ADVANCES IN HETEROCYCLIC CHEMISTRY 2022. [DOI: 10.1016/bs.aihch.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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24
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Chines S, Ehrt C, Potowski M, Biesenkamp F, Grützbach L, Brunner S, van den Broek F, Bali S, Ickstadt K, Brunschweiger A. Navigating chemical reaction space – application to DNA-encoded chemistry. Chem Sci 2022; 13:11221-11231. [PMID: 36320474 PMCID: PMC9517168 DOI: 10.1039/d2sc02474h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/31/2022] [Indexed: 12/02/2022] Open
Abstract
Databases contain millions of reactions for compound synthesis, rendering selection of reactions for forward synthetic design of small molecule screening libraries, such as DNA-encoded libraries (DELs), a big data challenge. To support reaction space navigation, we developed the computational workflow Reaction Navigator. Reaction files from a large chemistry database were processed using the open-source KNIME Analytics Platform. Initial processing steps included a customizable filtering cascade that removed reactions with a high probability to be incompatible with DEL, as they would e.g. damage the genetic barcode, to arrive at a comprehensive list of transformations for DEL design with applicability potential. These reactions were displayed and clustered by user-defined molecular reaction descriptors which are independent of reaction core substitution patterns. Thanks to clustering, these can be searched manually to identify reactions for DEL synthesis according to desired reaction criteria, such as ring formation or sp3 content. The workflow was initially applied for mapping chemical reaction space for aromatic aldehydes as an exemplary functional group often used in DEL synthesis. Exemplary reactions have been successfully translated to DNA-tagged substrates and can be applied to library synthesis. The versatility of the Reaction Navigator was then shown by mapping reaction space for different reaction conditions, for amines as a second set of starting materials, and for data from a second database. The computational tool Reaction Navigator supports chemical reaction space navigation by filtering and clustering reactions from chemistry databases. The utility of the tool was demonstrated by identification of reactions for DNA-encoded libraries.![]()
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Affiliation(s)
- Silvia Chines
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | | | - Marco Potowski
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Felix Biesenkamp
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Lars Grützbach
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Susanne Brunner
- TU Dortmund University, Department of Statistics, Vogelpothsweg 87, 44227, Dortmund, Germany
| | | | - Shilpa Bali
- Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands
| | - Katja Ickstadt
- TU Dortmund University, Department of Statistics, Vogelpothsweg 87, 44227, Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
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25
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Graham JS, Hunter JH, Waring MJ. Micellar Buchwald-Hartwig Coupling of Aryl and Heteroarylamines for the Synthesis of DNA-Encoded Libraries. J Org Chem 2021; 86:17257-17264. [PMID: 34788051 DOI: 10.1021/acs.joc.1c02325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA-encoded libraries are a very efficient means of identifying ligands for protein targets in high throughput. To fully maximize their use, it is essential to be able to carry out efficient reactions on DNA-conjugated substrates. Arylamines are privileged motifs in druglike molecules, and methods for their incorporation into DNA-encoded libraries are highly desirable. One of the preferred methods for their preparation, the Buchwald-Hartwig coupling, does not perform well on DNA conjugates using current approaches. We report the application of our recently developed micellar technology for on-DNA chemistry to the Buchwald-Hartwig reaction. Optimization of conditions led to a robust, high-yielding method for the synthesis of DNA-conjugated aryl and heteroarylamines, which is broad in substrate scope for both the arylamine and the DNA-conjugated aryl halide and is fully compatible with DNA-encoding and decoding procedures. This method will enable the preparation of diverse, high-fidelity libraries of biarylamines.
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Affiliation(s)
- Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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26
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Fair RJ, Walsh RT, Hupp CD. The expanding reaction toolkit for DNA-encoded libraries. Bioorg Med Chem Lett 2021; 51:128339. [PMID: 34478840 DOI: 10.1016/j.bmcl.2021.128339] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 12/30/2022]
Abstract
Over the past decade, DNA-encoded libraries (DELs) have emerged as a leading platform for small molecule drug discovery among pharmaceutical companies, biotech companies and academic drug hunters alike. This revolutionary technology has tremendous potential that is yet to be fully realized, as the exploration of therapeutically relevant chemical space is fueled by the ever-expanding repertoire of DNA-compatible reactions used to construct the libraries. Advances in direct coupling reactions, like photo-catalytic cross couplings, unique cyclizations such as the formation of 1,2,4-oxadiazoles, and new functional group transformations are valuable contributions to the DEL reaction toolkit, and indicate where future reaction development efforts should focus in order to maximize the productivity of DELs.
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Affiliation(s)
| | - Ryan T Walsh
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
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27
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemisch stabilisierte DNA‐Codes für DNA‐kodierte Chemie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Potowski
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Verena B. K. Kunig
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
| | - Lukas Eberlein
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Stefan M. Kast
- TU Dortmund University Faculty of Chemistry and Chemical Biology Physical Chemistry Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Andreas Brunschweiger
- TU Dortmund University Faculty of Chemistry and Chemical Biology Medicinal Chemistry Otto-Hahn-Straße 6 44227 Dortmund Deutschland
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28
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Potowski M, Kunig VBK, Eberlein L, Vakalopoulos A, Kast SM, Brunschweiger A. Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry. Angew Chem Int Ed Engl 2021; 60:19744-19749. [PMID: 34153170 PMCID: PMC8456907 DOI: 10.1002/anie.202104348] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/10/2021] [Indexed: 12/18/2022]
Abstract
DNA‐encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7‐deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson–Crick pairs, yielded ligation‐competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid‐ and metal ion‐promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid‐promoted Pictet–Spengler and Biginelli reactions, and metal‐promoted pyrazole syntheses on controlled pore glass‐coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification.
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Affiliation(s)
- Marco Potowski
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Verena B K Kunig
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Lukas Eberlein
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | | | - Stefan M Kast
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
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29
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Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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Hunter JH, Anderson MJ, Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Crawford JJ, Madin A, Pairaudeau G, Waring MJ. Highly efficient on-DNA amide couplings promoted by micelle forming surfactants for the synthesis of DNA encoded libraries. Chem Sci 2021; 12:9475-9484. [PMID: 34349922 PMCID: PMC8278914 DOI: 10.1039/d1sc03007h] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
DNA encoded libraries (DELs) represent powerful new technology for finding small molecule ligands for proteins and are increasingly being applied to hit finding in medicinal chemistry. Crucial to the synthesis of high quality DELs is the identification of chemical reactions for their assembly that proceed with very high conversion across a range of different substrates, under conditions compatible with DNA-tagged substrates. Many current chemistries used in DEL synthesis do not meet this requirement, resulting in libraries of low fidelity. Amide couplings are the most commonly used reaction in synthesis of screening libraries and also in DELs. The ability to carry out highly efficient, widely applicable amide couplings in DEL synthesis would therefore be highly desirable. We report a method for amide coupling using micelle forming surfactants, promoted by a modified linker, that is broadly applicable across a wide range of substrates. Most significantly, this works exceptionally well for coupling of DNA-conjugated carboxylic acids (N-to-C) with amines in solution, a procedure that is currently very inefficient. The optimisation of separate procedures for coupling of DNA-conjugated acids and amines by reagent screening and statistically driven optimisation is described. The generality of the method is illustrated by the application to a wide range of examples with unprecedented levels of conversion. The utility of the (N-to-C) coupling of DNA-conjugated acids in DEL synthesis is illustrated by the three cycle synthesis of a fully DNA-encoded compound by two cycles of coupling of an aminoester, with intermediate ester hydrolysis, followed by capping with an amine. This methodology will be of great utility in the synthesis of high fidelity DELs.
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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 UK
| | - Matthew J Anderson
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
| | - James J Crawford
- Department of Discovery Chemistry, Genentech Inc. 1 DNA Way South San Francisco CA 94080 USA
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge CB4 0WG UK
| | - Garry Pairaudeau
- Exscientia Schrödinger Building, Oxford Science Park Oxford OX4 4GE UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
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Klika Škopić M, Gramse C, Oliva R, Pospich S, Neukirch L, Manisegaran M, Raunser S, Winter R, Weberskirch R, Brunschweiger A. Towards DNA-Encoded Micellar Chemistry: DNA-Micelle Association and Environment Sensitivity of Catalysis. Chemistry 2021; 27:10048-10057. [PMID: 33979454 PMCID: PMC8361662 DOI: 10.1002/chem.202100980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 02/06/2023]
Abstract
The development of DNA-compatible reaction methodologies is a central theme to advance DNA-encoded screening library technology. Recently, we were able to show that sulfonic acid-functionalized block copolymer micelles facilitated Brønsted acid-promoted reactions such as the Povarov reaction on DNA-coupled starting materials with minimal DNA degradation. Here, the impact of polymer composition on micelle shape, and reaction conversion was investigated. A dozen sulfonic acid-functionalized block copolymers of different molar mass and composition were prepared by RAFT polymerization and were tested in the Povarov reaction, removal of the Boc protective group, and the Biginelli reaction. The results showed trends in the polymer structure-micellar catalytic activity relationship. For instance, micelles composed of block copolymers with shorter acrylate ester chains formed smaller particles and tended to provide faster reaction kinetics. Moreover, fluorescence quenching experiments as well as circular dichroism spectroscopy showed that DNA-oligomer-conjugates, although highly water-soluble, accumulated very effectively in the micellar compartments, which is a prerequisite for carrying out a DNA-encoded reaction in the presence of polymer micelles.
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Affiliation(s)
- Mateja Klika Škopić
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Christian Gramse
- Polymer Hybrid SystemsFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Rosario Oliva
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Sabrina Pospich
- Department of Structural BiochemistryMax Planck Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
| | - Laura Neukirch
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Magiliny Manisegaran
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Stefan Raunser
- Department of Structural BiochemistryMax Planck Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
| | - Roland Winter
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Ralf Weberskirch
- Polymer Hybrid SystemsFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Andreas Brunschweiger
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
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Lenci E, Baldini L, Trabocchi A. Diversity-oriented synthesis as a tool to expand the chemical space of DNA-encoded libraries. Bioorg Med Chem 2021; 41:116218. [PMID: 34030087 DOI: 10.1016/j.bmc.2021.116218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022]
Abstract
DNA-encoded libraries (DEL) represent a powerful technology for generating compound collections for drug discovery campaigns, that have allowed for the selection of many hit compounds over last three decades. However, the application of split-and-pool combinatorial methodologies, as well as the limitation imposed by DNA-compatible chemistry, has often brought to a limited exploration of the chemical space, with an over-representation of flat aromatic or peptide-like structures, whereas a higher scaffold complexity is generally associated with a more successful biological activity of the library. In this context, the application of Diversity-Oriented Synthesis, capable of creating sp3-rich molecular entities even starting from simple flat building blocks, can represent an efficient strategy to significantly broaden the chemical space explored by DELs. In this review, we present selected examples of DNA-compatible complexity-generating reactions that can be applied for the generation of DNA-encoded DOS libraries, including: (i) multicomponent reactions; (ii) C-H/C-X functionalization; (iii) tandem approaches; (iv) cycloadditions; (v) reactions introducing privileged elements. Also, selected case studies on the generation of DELs with high scaffold diversity are discussed, reporting their application in drug discovery programs.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Baldini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy; Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM), University of Florence, Viale Morgagni 85, 50134 Florence, Italy.
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Haarr MB, Sydnes MO. Synthesis of the Hexahydropyrrolo-[3,2-c]-quinoline Core Structure and Strategies for Further Elaboration to Martinelline, Martinellic Acid, Incargranine B, and Seneciobipyrrolidine. Molecules 2021; 26:molecules26020341. [PMID: 33440776 PMCID: PMC7827258 DOI: 10.3390/molecules26020341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 02/03/2023] Open
Abstract
Natural products are rich sources of interesting scaffolds possessing a plethora of biological activity. With the isolation of the martinella alkaloids in 1995, namely martinelline and martinellic acid, the pyrrolo[3,2-c]quinoline scaffold was discovered. Since then, this scaffold has been found in two additional natural products, viz. incargranine B and seneciobipyrrolidine. These natural products have attracted attention from synthetic chemists both due to the interesting scaffold they contain, but also due to the biological activity they possess. This review highlights the synthetic efforts made for the preparation of these alkaloids and formation of analogues with interesting biological activity.
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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: 59] [Impact Index Per Article: 19.7] [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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Wang X, Liu J, Yan Z, Liu X, Liu S, Suo Y, Lu W, Yue J, Chen K, Jiang H, Zhao Y, Zheng M, Dai D, Lu X. Diversified strategy for the synthesis of DNA-encoded oxindole libraries. Chem Sci 2021; 12:2841-2847. [PMID: 34164048 PMCID: PMC8179416 DOI: 10.1039/d0sc06696f] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA-encoded library technology (DELT) employs DNA as a barcode to track the sequence of chemical reactions and enables the design and synthesis of libraries with billions of small molecules through combinatorial expansion. This powerful technology platform has been successfully demonstrated for hit identification and target validation for many types of diseases. As a highly integrated technology platform, DEL is capable of accelerating the translation of synthetic chemistry by using on-DNA compatible reactions or off-DNA scaffold synthesis. Herein, we report the development of a series of novel on-DNA transformations based on oxindole scaffolds for the design and synthesis of diversity-oriented DNA-encoded libraries for screening. Specifically, we have developed 1,3-dipolar cyclizations, cyclopropanations, ring-opening of reactions of aziridines and Claisen–Schmidt condensations to construct diverse oxindole derivatives. The majority of these transformations enable a diversity-oriented synthesis of DNA-encoded oxindole libraries which have been used in the successful hit identification for three protein targets. We have demonstrated that a diversified strategy for DEL synthesis could accelerate the application of synthetic chemistry for drug discovery. Constructing DNA-encoded oxindole libraries by a diversified strategy.![]()
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 P. R. China .,Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd. 4560 Jinke Road, Building No. 2, 13th Floor, Pudong Shanghai 201210 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
| | - Ziqin Yan
- 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
| | - Xiaohong Liu
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University Pudong Shanghai 201210 P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 P. R. China.,University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 P. R. China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 P. R. China
| | - 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 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
| | - 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 P. R. China
| | - Kaixian Chen
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University Pudong Shanghai 201210 P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 P. R. China.,University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 P. R. China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University Pudong Shanghai 201210 P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 P. R. China.,University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 P. R. China
| | - Yujun Zhao
- 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
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road Shanghai 201203 P. R. China.,University of Chinese Academy of Sciences No. 19A Yuquan Road Beijing 100049 P. R. China
| | - Dongcheng Dai
- Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd. 4560 Jinke Road, Building No. 2, 13th Floor, Pudong Shanghai 201210 P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong Shanghai 201203 P. R. China
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Nghiem TL, Coban D, Tjaberings S, Gröschel AH. Recent Advances in the Synthesis and Application of Polymer Compartments for Catalysis. Polymers (Basel) 2020; 12:E2190. [PMID: 32987965 PMCID: PMC7600123 DOI: 10.3390/polym12102190] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Catalysis is one of the most important processes in nature, science, and technology, that enables the energy efficient synthesis of essential organic compounds, pharmaceutically active substances, and molecular energy sources. In nature, catalytic reactions typically occur in aqueous environments involving multiple catalytic sites. To prevent the deactivation of catalysts in water or avoid unwanted cross-reactions, catalysts are often site-isolated in nanopockets or separately stored in compartments. These concepts have inspired the design of a range of synthetic nanoreactors that allow otherwise unfeasible catalytic reactions in aqueous environments. Since the field of nanoreactors is evolving rapidly, we here summarize-from a personal perspective-prominent and recent examples for polymer nanoreactors with emphasis on their synthesis and their ability to catalyze reactions in dispersion. Examples comprise the incorporation of catalytic sites into hydrophobic nanodomains of single chain polymer nanoparticles, molecular polymer nanoparticles, and block copolymer micelles and vesicles. We focus on catalytic reactions mediated by transition metal and organocatalysts, and the separate storage of multiple catalysts for one-pot cascade reactions. Efforts devoted to the field of nanoreactors are relevant for catalytic chemistry and nanotechnology, as well as the synthesis of pharmaceutical and natural compounds. Optimized nanoreactors will aid in the development of more potent catalytic systems for green and fast reaction sequences contributing to sustainable chemistry by reducing waste of solvents, reagents, and energy.
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Affiliation(s)
| | | | | | - André H. Gröschel
- Physical Chemistry and Centre for Soft Nanoscience (SoN), University of Münster, 48149 Münster, Germany; (T.-L.N.); (D.C.); (S.T.)
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Fan Z, Zhao S, Liu T, Shen PX, Cui ZN, Zhuang Z, Shao Q, Chen JS, Ratnayake AS, Flanagan ME, Kölmel DK, Piotrowski DW, Richardson P, Yu JQ. Merging C(sp 3)-H activation with DNA-encoding. Chem Sci 2020; 11:12282-12288. [PMID: 34094436 PMCID: PMC8162953 DOI: 10.1039/d0sc03935g] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA-encoded library (DEL) technology has the potential to dramatically expedite hit identification in drug discovery owing to its ability to perform protein affinity selection with millions or billions of molecules in a few experiments. To expand the molecular diversity of DEL, it is critical to develop different types of DNA-encoded transformations that produce billions of molecules with distinct molecular scaffolds. Sequential functionalization of multiple C–H bonds provides a unique avenue for creating diversity and complexity from simple starting materials. However, the use of water as solvent, the presence of DNA, and the extremely low concentration of DNA-encoded coupling partners (0.001 M) have hampered the development of DNA-encoded C(sp3)–H activation reactions. Herein, we report the realization of palladium-catalyzed C(sp3)–H arylation of aliphatic carboxylic acids, amides and ketones with DNA-encoded aryl iodides in water. Notably, the present method enables the use of alternative sets of monofunctional building blocks, providing a linchpin to facilitate further setup for DELs. Furthermore, the C–H arylation chemistry enabled the on-DNA synthesis of structurally-diverse scaffolds containing enriched C(sp3) character, chiral centers, cyclopropane, cyclobutane, and heterocycles. DNA-compatible C(sp3)–H activation reactions of aliphatic carboxylic acids, amides, and ketones were developed for efficient access to DEL synthesis.![]()
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Affiliation(s)
- Zhoulong Fan
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Shuai Zhao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Tao Liu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Peng-Xiang Shen
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zi-Ning Cui
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zhe Zhuang
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Qian Shao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Anokha S Ratnayake
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Mark E Flanagan
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Dominik K Kölmel
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - David W Piotrowski
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive San Diego CA 09121 USA
| | - Jin-Quan Yu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
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Pashirova TN, Fetin PA, Lezov AA, Kadnikov MV, Valeeva FG, Burilova EA, Bilibin AY, Zorin IM. Self-Assembled Quaternary Ammonium-Containing Comb-Like Polyelectrolytes for the Hydrolysis of Organophosphorous Esters: Effect of Head Groups and Counter-Ions. Chempluschem 2020; 85:1939-1948. [PMID: 32865345 DOI: 10.1002/cplu.202000417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/27/2020] [Indexed: 12/17/2022]
Abstract
The aim of this work was to increase the efficiency of catalytic systems for the hydrolytic cleavage of 4-nitrophenyl esters of phosphonic acids. Quaternary ammonium-containing comb-like polyelectrolytes («polymerized micelles») with ester cleavable fragments and a low aggregation threshold were used as catalysts. The synthesis of poly(11-acryloyloxyundecylammonium) surfactants with different counterions (Br- , NO3 - , CH3 C6 H4 SO3 - ) and head groups was realized by micellar free-radical polymerization. Molecular weight, critical association concentration, particle sizes and solubilization properties toward Orange OT were determined. Self-assemblies organized by poly(11-acryloyloxyundecyltrimethyl ammonium) bromide successfully catalyze the hydrolysis of 4-nitrophenyl butylchloromethylphosphonate up to two orders of magnitude compared to aqueous alkaline hydrolysis. The development of these catalysts is promising for industrial applications and organophosphorus compound detoxification.
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Affiliation(s)
- Tatiana N Pashirova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov St., 8, Kazan, 420088, Russian Federation
| | - Petr A Fetin
- Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab, St., Petersburg, 199034, Russian Federation
| | - Alexey A Lezov
- Department of Molecular Biophysics and Polymer Physics, Physical Faculty, St. Petersburg State University, 7/9 Universitetskaya nab, St., Petersburg, 199034, Russian Federation
| | - Matvey V Kadnikov
- Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab, St., Petersburg, 199034, Russian Federation
| | - Farida G Valeeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov St., 8, Kazan, 420088, Russian Federation
| | - Evgenia A Burilova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov St., 8, Kazan, 420088, Russian Federation
| | - Alexander Yu Bilibin
- Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab, St., Petersburg, 199034, Russian Federation
| | - Ivan M Zorin
- Institute of Chemistry, St. Petersburg State University, 7/9 Universitetskaya nab, St., Petersburg, 199034, Russian Federation
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39
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Gerry CJ, Schreiber SL. Recent achievements and current trajectories of diversity-oriented synthesis. Curr Opin Chem Biol 2020; 56:1-9. [DOI: 10.1016/j.cbpa.2019.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
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40
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Li K, Liu X, Liu S, An Y, Shen Y, Sun Q, Shi X, Su W, Cui W, Duan Z, Kuai L, Yang H, Satz AL, Chen K, Jiang H, Zheng M, Peng X, Lu X. Solution-Phase DNA-Compatible Pictet-Spengler Reaction Aided by Machine Learning Building Block Filtering. iScience 2020; 23:101142. [PMID: 32446221 PMCID: PMC7243192 DOI: 10.1016/j.isci.2020.101142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 02/05/2023] Open
Abstract
The application of machine learning toward DNA encoded library (DEL) technology is lacking despite obvious synergy between these two advancing technologies. Herein, a machine learning algorithm has been developed that predicts the conversion rate for the DNA-compatible reaction of a building block with a model DNA-conjugate. We exemplify the value of this technique with a challenging reaction, the Pictet-Spengler, where acidic conditions are normally required to achieve the desired cyclization between tryptophan and aldehydes to provide tryptolines. This is the first demonstration of using a machine learning algorithm to cull potential building blocks prior to their purchase and testing for DNA-encoded library synthesis. Importantly, this allows for a challenging reaction, with an otherwise very low building block pass rate in the test reaction, to still be used in DEL synthesis. Furthermore, because our protocol is solution phase it is directly applicable to standard plate-based DEL synthesis. A mild solution-phase, plate applicable DNA-compatible Pictet-Spengler (PS) reaction An efficient strategy for DNA-encoded diversified tryptoline libraries synthesis A machine learning algorithm of building blocks filtering for DEL synthesis An elegant application of machine learning for DNA-encoded library technology
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Affiliation(s)
- Ke Li
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaohong Liu
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yulong An
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yanfang Shen
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qingxia Sun
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Letian Kuai
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L Satz
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Kaixian Chen
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
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41
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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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42
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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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43
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Westphal MV, Hudson L, Mason JW, Pradeilles JA, Zécri FJ, Briner K, Schreiber SL. Water-Compatible Cycloadditions of Oligonucleotide-Conjugated Strained Allenes for DNA-Encoded Library Synthesis. J Am Chem Soc 2020; 142:7776-7782. [PMID: 32267148 DOI: 10.1021/jacs.9b13186] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA-encoded libraries of small molecules are being explored extensively for the identification of binders in early drug-discovery efforts. Combinatorial syntheses of such libraries require water- and DNA-compatible reactions, and the paucity of these reactions currently limit the chemical features of resulting barcoded products. The present work introduces strain-promoted cycloadditions of cyclic allenes under mild conditions to DNA-encoded library synthesis. Owing to distinct cycloaddition modes of these reactive intermediates with activated olefins, 1,3-dipoles, and dienes, the process generates diverse molecular architectures from a single precursor. The resulting DNA-barcoded compounds exhibit unprecedented ring and topographic features, related to elements found to be powerful in phenotypic screening.
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Affiliation(s)
- Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Johan A Pradeilles
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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44
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Potowski M, Esken R, Brunschweiger A. Translation of the copper/bipyridine-promoted Petasis reaction to solid phase-coupled DNA for encoded library synthesis. Bioorg Med Chem 2020; 28:115441. [PMID: 32222338 DOI: 10.1016/j.bmc.2020.115441] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/28/2020] [Accepted: 03/12/2020] [Indexed: 11/28/2022]
Abstract
The Petasis three-component reaction gives rise to diverse substituted α-aryl glycines from readily available amines, boronic acids and glyoxalic acid. Thus, this reaction is highly attractive for DNA-encoded small molecule screening library synthesis. The Petasis reaction is for instance promoted by a potentially DNA damaging copper(I)/bipyridine reagent system in dry organic solvents. We found that solid phase-coupled DNA strands tolerated this reagent system at elevated temperature allowing for synthesis of diverse substituted DNA-tagged α-aryl glycines from DNA-conjugated secondary amines.
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Affiliation(s)
- Marco Potowski
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Robin Esken
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, D 44227 Dortmund, Germany.
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45
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Bobers J, Škopić MK, Dinter R, Sakthithasan P, Neukirch L, Gramse C, Weberskirch R, Brunschweiger A, Kockmann N. Design of an Automated Reagent-Dispensing System for Reaction Screening and Validation with DNA-Tagged Substrates. ACS COMBINATORIAL SCIENCE 2020; 22:101-108. [PMID: 32053337 DOI: 10.1021/acscombsci.9b00207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Laboratory automation strategies have vast potential for accelerating discovery processes. They enable higher efficiency and throughput for time-consuming screening procedures and reduce error-prone manual steps. Automating repetitive procedures can for instance support chemists in optimizing chemical reactions. Particularly, the technology of DNA-encoded libraries (DELs) may benefit from automation techniques, since translation of chemical reactions to DNA-tagged reactants often requires screening of multiple reaction parameters and evaluation of large numbers of reactants. Here, we describe a portable, automated system for reagent dispensing that was designed from open source materials. The system was validated by performing amide coupling of carboxylic acids to DNA-linked amine and a micelle-mediated Povarov reaction to DNA-tagged hexahydropyrroloquinolines. The latter reaction required accurate pipetting of multiple components including different solvents and a surface-active reagent. Analysis of reactions demonstrated that the robotic system achieved high accuracy comparable to experimentation by an experienced chemist with the potential of higher throughput.
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Affiliation(s)
- Jens Bobers
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Mateja Klika Škopić
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Robin Dinter
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Piriyanth Sakthithasan
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
| | - Laura Neukirch
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Christian Gramse
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Ralf Weberskirch
- Faculty of Chemistry and Chemical Biology, Polymer Hybrid Systems, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Andreas Brunschweiger
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Medicinal Chemistry, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Norbert Kockmann
- TU Dortmund University, Department of Chemical and Biochemical Engineering, Laboratory of Equipment Design, Emil-Figge-Strasse 68, 44227 Dortmund, Germany
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46
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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47
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Flood DT, Kingston C, Vantourout JC, Dawson PE, Baran PS. DNA Encoded Libraries: A Visitor's Guide. Isr J Chem 2020. [DOI: 10.1002/ijch.201900133] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dillon T. Flood
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Cian Kingston
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Julien C. Vantourout
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Philip E. Dawson
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
| | - Phil S. Baran
- Department of ChemistryScripps Research 10550 North Torrey Pines Road La Jolla, California 93037
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48
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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: 33] [Impact Index Per Article: 8.3] [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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49
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Wang H, Wang Y, Han Y, Zhao W, Wang X. Humic acid as an efficient and reusable catalyst for one pot three-component green synthesis of 5-substituted 1H-tetrazoles in water. RSC Adv 2020; 10:784-789. [PMID: 35494449 PMCID: PMC9047532 DOI: 10.1039/c9ra08523h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
A simple one pot three-component green synthesis of 5-substituted 1H-tetrazoles is described using humic acid as an efficient catalyst in water.
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Affiliation(s)
- Hongshe Wang
- College of Chemistry and Chemical Engineering
- Baoji University of Arts and Sciences
- Baoji 721013
- China
| | - Yichun Wang
- College of Pharmacy
- Shaanxi University of Chinese Medicine
- Xianyang 712046
- China
| | - Yinfeng Han
- College of Chemistry and Chemical Engineering
- Baoji University of Arts and Sciences
- Baoji 721013
- China
| | - Weixing Zhao
- College of Chemistry and Chemical Engineering
- Baoji University of Arts and Sciences
- Baoji 721013
- China
| | - Xiaomei Wang
- College of Chemistry and Chemical Engineering
- Baoji University of Arts and Sciences
- Baoji 721013
- China
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50
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Zambaldo C, Geigle SN, Satz AL. High-Throughput Solid-Phase Building Block Synthesis for DNA-Encoded Libraries. Org Lett 2019; 21:9353-9357. [PMID: 31747291 DOI: 10.1021/acs.orglett.9b03553] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we provide a generalizable method for the cost-effective synthesis of thousands of building blocks (BBs) employing DNA-incompatible chemistries. The ability to produce large numbers of crude products via solid-phase synthesis has existed for decades; however, our work demonstrates a practical use of such crude reaction mixtures and employs DNA-conjugation to simultaneously encode, purify, and rapidly analyze the desired products. This workflow generated sp3-rich BBs that could be encoded by DNA in a high-throughput manner.
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