101
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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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102
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Li K, Qu Y, An Y, Breinlinger E, Webster MP, Wen H, Ding D, Zhao M, Shi X, Wang J, Su W, Cui W, Satz AL, Yang H, Kuai L, Little A, Peng X. DNA-Compatible Copper-Catalyzed Oxidative Amidation of Aldehydes with Non-Nucleophilic Arylamines. Bioconjug Chem 2020; 31:2092-2097. [DOI: 10.1021/acs.bioconjchem.0c00392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ke Li
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Yi Qu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Eric Breinlinger
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Matthew P. Webster
- Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Huanan Wen
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Duanchen Ding
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Meng Zhao
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xiaodong Shi
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Jiangong Wang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Alexander L. Satz
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Andrew Little
- AbbVie Bioresearch Center, 381 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
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103
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Lemke M, Ravenscroft H, Rueb NJ, Kireev D, Ferraris D, Franzini RM. Integrating DNA-encoded chemical libraries with virtual combinatorial library screening: Optimizing a PARP10 inhibitor. Bioorg Med Chem Lett 2020; 30:127464. [PMID: 32768646 DOI: 10.1016/j.bmcl.2020.127464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/25/2020] [Accepted: 08/02/2020] [Indexed: 12/17/2022]
Abstract
Two critical steps in drug development are 1) the discovery of molecules that have the desired effects on a target, and 2) the optimization of such molecules into lead compounds with the required potency and pharmacokinetic properties for translation. DNA-encoded chemical libraries (DECLs) can nowadays yield hits with unprecedented ease, and lead-optimization is becoming the limiting step. Here we integrate DECL screening with structure-based computational methods to streamline the development of lead compounds. The presented workflow consists of enumerating a virtual combinatorial library (VCL) derived from a DECL screening hit and using computational binding prediction to identify molecules with enhanced properties relative to the original DECL hit. As proof-of-concept demonstration, we applied this approach to identify an inhibitor of PARP10 that is more potent and druglike than the original DECL screening hit.
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Affiliation(s)
- Mike Lemke
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA
| | - Hannah Ravenscroft
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA
| | - Nicole J Rueb
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT 84112, USA
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Dana Ferraris
- Department of Chemistry, McDaniel College, 2 College Hill, Westminster, MD 21157, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT 84112, USA.
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104
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Hamada S. Organic Synthesis for Diversity Expansion of DNA Encoded Libraries. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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105
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Bao Y, Deng Z, Feng J, Zhu W, Li J, Wan J, Liu G. A B 2(OH) 4-Mediated Synthesis of 2-Substituted Indazolone and Its Application in a DNA-Encoded Library. Org Lett 2020; 22:6277-6282. [PMID: 32806212 DOI: 10.1021/acs.orglett.0c02032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indazolone cores are among the most common structural components in medicinal chemistry and can be found in many biologically active molecules. In this report, a mild and efficient approach to 2-substituted indazolones via B2(OH)4-mediated reductive N-N bond formation is developed. This strategy features mild conditions, no request for a metal catalyst, and a wide scope for both aliphatic and aromatic amines. Meanwhile, this method was further successfully applied on DNA to construct indazolone cores for a DNA-encoded library. This will enable the production of a very attractive indazolone-cored library from simple amines and scaffolds, which will provide considerable diversity.
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Affiliation(s)
- Yapeng Bao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Zongfa Deng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Weiwei Zhu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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106
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Buskes MJ, Blanco MJ. Impact of Cross-Coupling Reactions in Drug Discovery and Development. Molecules 2020; 25:E3493. [PMID: 32751973 PMCID: PMC7436090 DOI: 10.3390/molecules25153493] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022] Open
Abstract
Cross-coupling reactions have played a critical role enabling the rapid expansion of structure-activity relationships (SAR) during the drug discovery phase to identify a clinical candidate and facilitate subsequent drug development processes. The reliability and flexibility of this methodology have attracted great interest in the pharmaceutical industry, becoming one of the most used approaches from Lead Generation to Lead Optimization. In this mini-review, we present an overview of cross-coupling reaction applications to medicinal chemistry efforts, in particular the Suzuki-Miyaura and Buchwald-Hartwig cross-coupling reactions as a remarkable resource for the generation of carbon-carbon and carbon-heteroatom bonds. To further appreciate the impact of this methodology, the authors discuss some recent examples of clinical candidates that utilize key cross-coupling reactions in their large-scale synthetic process. Looking into future opportunities, the authors highlight the versatility of the cross-coupling reactions towards new chemical modalities like DNA-encoded libraries (DELs), new generation of peptides and cyclopeptides, allosteric modulators, and proteolysis targeting chimera (PROTAC) approaches.
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Affiliation(s)
| | - Maria-Jesus Blanco
- Medicinal Chemistry. Sage Therapeutics, Inc. 215 First Street, Cambridge, MA 02142, USA;
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107
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Wen X, Duan Z, Liu J, Lu W, Lu X. On-DNA Cross-Dehydrogenative Coupling Reaction toward the Synthesis of Focused DNA-Encoded Tetrahydroisoquinoline Libraries. Org Lett 2020; 22:5721-5725. [DOI: 10.1021/acs.orglett.0c01565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Jiaxiang Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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108
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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.
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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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109
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
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110
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Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020; 59:14965-14972. [PMID: 32436364 DOI: 10.1002/anie.202005070] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Indexed: 11/11/2022]
Abstract
Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.
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Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China.,Department of Chemistry, Southern University of Science and Technology China, 1088 Xueyuan Road, Shenzhen, China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
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111
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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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112
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Qu Y, Wen H, Ge R, Xu Y, Gao H, Shi X, Wang J, Cui W, Su W, Yang H, Kuai L, Satz AL, Peng X. Copper-Mediated DNA-Compatible One-Pot Click Reactions of Alkynes with Aryl Borates and TMS-N3. Org Lett 2020; 22:4146-4150. [DOI: 10.1021/acs.orglett.0c01219] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Qu
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Huanan Wen
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Rui Ge
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yanfen Xu
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hong Gao
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jiangong Wang
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L. Satz
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xuanjia Peng
- HitS Business Unit, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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113
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An YL, Li K, Shen Y, Hong Z, Chen L, Hu Y, Zhou L, Wang D, Shi X, Liu S, Su W, Cui W, Kuai L, Yang H, Peng X. DNA Compatible Intermolecular Wittig Olefination for the Construction of α, β-Unsaturated Carbonyl Compounds. Org Lett 2020; 22:3931-3935. [DOI: 10.1021/acs.orglett.0c01215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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114
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Zhou Y, Peng J, Shen W, Li X. Psoralen as an interstrand DNA crosslinker in the selection of DNA-Encoded dynamic chemical library. Biochem Biophys Res Commun 2020; 533:215-222. [PMID: 32359876 DOI: 10.1016/j.bbrc.2020.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/04/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful technology for ligand discovery in biomedical research. Recently, we have developed a DNA-encoded dynamic library (DEDL) approach by incorporating the concept of dynamic combinatorial library (DCL) with DELs. DEDL has shown excellent potential in ligand discovery towards a variety of protein targets. However, the requirement of having a pair of unnatural p-stilbazoles as the interstrand DNA crosslinker has limited the chemical diversity of DEDLs. Here, we replaced p-stilbazole with psoralen (PS) and tested the feasibility of psoralen as the crosslinker in DEDL selection. Since psoralen is commercially available and does not require any special crosslinking partner, existing DELs may be directly used to create high-diversity DEDLs. This study is expected to greatly facilitate the development of DEDLs as a versatile tool in drug discovery.
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Affiliation(s)
- Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China; Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, 518055, China
| | - Wenyin Shen
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
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115
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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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116
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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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117
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Sannino A, Gironda-Martínez A, Gorre ÉMD, Prati L, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections. ACS COMBINATORIAL SCIENCE 2020; 22:204-212. [PMID: 32109359 DOI: 10.1021/acscombsci.0c00023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growing importance of DNA-encoded chemical libraries (DECLs) as tools for the discovery of protein binders has sparked an interest for the development of efficient screening methodologies, capable of discriminating between high- and medium-affinity ligands. Here, we present a systematic investigation of selection methodologies, featuring a library displayed on single-stranded DNA, which could be hybridized to a complementary oligonucleotide carrying a diazirine photoreactive group. Model experiments, performed using ligands of different affinity to carbonic anhydrase IX, revealed a recovery of preferential binders up to 10%, which was mainly limited by the highly reactive nature of carbene intermediates generated during the photo-cross-linking process. Ligands featuring acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared to their counterparts based on 3-sulfamoyl benzoic acid, which had a lower affinity toward the target. A systematic evaluation of experimental parameters revealed conditions that were ideally suited for library screening, which were used for the screening of a combinatorial DECL library, featuring 669 240 combinations of two sets of building blocks. Compared to conventional affinity capture procedures on protein immobilized on solid supports, photo-cross-linking provided a better discrimination of low-affinity CAIX ligands over the background signal and therefore can be used as a tandem methodology with the affinity capture procedures.
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Affiliation(s)
| | | | | | - Luca Prati
- Philochem AG, 8112 Otelfingen, Switzerland
| | | | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
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118
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Wu W, Sun Z, Wang X, Lu X, Dai D. Construction of Thiazole-Fused Dihydropyrans via Formal [4 + 2] Cycloaddition Reaction on DNA. Org Lett 2020; 22:3239-3244. [PMID: 32243186 DOI: 10.1021/acs.orglett.0c01016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient and facile formal [4 + 2] cycloaddition reaction was developed to synthesize diverse thiazole-fused dihydropyrans (TFDP) on DNA. Mild reaction conditions, broad substrate scope, and compatibility with subsequent enzymatic ligation demonstrated the utility of this methodology in DNA-encoded library synthesis.
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Affiliation(s)
- Wenting Wu
- Department of Therapeutic Discovery, Amgen Asia R&D Center, Amgen Research, 4560 Jinke Road, Pudong, Shanghai 201210, P. R. China
| | - Zhen Sun
- Department of Therapeutic Discovery, Amgen Asia R&D Center, Amgen Research, 4560 Jinke Road, Pudong, Shanghai 201210, P. R. China
| | - Xuan Wang
- Department of Therapeutic Discovery, Amgen Asia R&D Center, Amgen Research, 4560 Jinke Road, Pudong, Shanghai 201210, P. R. China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Dongcheng Dai
- Department of Therapeutic Discovery, Amgen Asia R&D Center, Amgen Research, 4560 Jinke Road, Pudong, Shanghai 201210, P. R. China
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119
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Kölmel DK, Ratnayake AS, Flanagan ME, Tsai MH, Duan C, Song C. Photocatalytic [2 + 2] Cycloaddition in DNA-Encoded Chemistry. Org Lett 2020; 22:2908-2913. [PMID: 32239950 DOI: 10.1021/acs.orglett.0c00574] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The on-DNA synthesis of highly substituted cyclobutanes was achieved through a photocatalytic [2 + 2] cycloaddition reaction in aqueous solution. Readily available DNA-tagged styrene derivatives were reacted with structurally diverse cinnamates in the presence of an iridium-based photocatalyst, Ir(ppy)2(dtbbpy)PF6, to forge two new C(sp3)-C(sp3) bonds. This transformation was demonstrated to have excellent functional group tolerance and allowed for the facile installation of a variety of heteroaromatic substituents on a densely functionalized cyclobutane scaffold.
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Affiliation(s)
- Dominik K Kölmel
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mei-Hsuan Tsai
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Cong Duan
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Chao Song
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
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120
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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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121
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Flood DT, Zhang X, Fu X, Zhao Z, Asai S, Sanchez BB, Sturgell EJ, Vantourout JC, Richardson P, Flanagan ME, Piotrowski DW, Kölmel DK, Wan J, Tsai MH, Chen JS, Baran PS, Dawson PE. RASS-Enabled S/P-C and S-N Bond Formation for DEL Synthesis. Angew Chem Int Ed Engl 2020; 59:7377-7383. [PMID: 32050046 DOI: 10.1002/anie.201915493] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/05/2020] [Indexed: 01/28/2023]
Abstract
DNA encoded libraries (DEL) have shown promise as a valuable technology for democratizing the hit discovery process. Although DEL provides relatively inexpensive access to libraries of unprecedented size, their production has been hampered by the idiosyncratic needs of the encoding DNA tag relegating DEL compatible chemistry to dilute aqueous environments. Recently reversible adsorption to solid support (RASS) has been demonstrated as a promising method to expand DEL reactivity using standard organic synthesis protocols. Here we demonstrate a suite of on-DNA chemistries to incorporate medicinally relevant and C-S, C-P and N-S linkages into DELs, which are underrepresented in the canonical methods.
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Affiliation(s)
- Dillon T Flood
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Xuejing Zhang
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.,School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiang Fu
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.,School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhenxiang Zhao
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Shota Asai
- Department of Chemistry and Biological Sciences, Faculty of and Engineering, Iwate University, 4-3-5 Ueda, Morioka, 020-8551, Japan
| | - Brittany B Sanchez
- Automated Synthesis Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Emily J Sturgell
- Automated Synthesis Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Julien C Vantourout
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Mark E Flanagan
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT, 06340, USA
| | | | - Dominik K Kölmel
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT, 06340, USA
| | - Jinqiao Wan
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, China
| | - Mei-Hsuan Tsai
- HitGen Inc., Building 6, No. 8 Huigu 1st East Road Tianfu International Bio-Town, Shuangliu District, Chengdu, 610200, Sichuan, China
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Philip E Dawson
- Department of Chemistry, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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122
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Flood DT, Zhang X, Fu X, Zhao Z, Asai S, Sanchez BB, Sturgell EJ, Vantourout JC, Richardson P, Flanagan ME, Piotrowski DW, Kölmel DK, Wan J, Tsai M, Chen JS, Baran PS, Dawson PE. RASS‐Enabled S/P−C and S−N Bond Formation for DEL Synthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Dillon T. Flood
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Xuejing Zhang
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
- School of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 China
| | - Xiang Fu
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
- School of Pharmaceutical SciencesSun Yat-sen University Guangzhou 510006 China
| | - Zhenxiang Zhao
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Shota Asai
- Department of Chemistry and Biological SciencesFaculty of and EngineeringIwate University 4-3-5 Ueda Morioka 020-8551 Japan
| | - Brittany B. Sanchez
- Automated Synthesis FacilityThe Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Emily J. Sturgell
- Automated Synthesis FacilityThe Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Julien C. Vantourout
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Paul Richardson
- Pfizer Medicinal Chemistry 10770 Science Center Drive San Diego CA 92121 USA
| | - Mark E. Flanagan
- Pfizer Medicinal Chemistry Eastern Point Road Groton CT 06340 USA
| | | | | | - Jinqiao Wan
- HitGen Inc. Building 6, No. 8 Huigu 1st East Road Tianfu International Bio-Town, Shuangliu District, Chengdu 610200 Sichuan China
| | - Mei‐Hsuan Tsai
- HitGen Inc. Building 6, No. 8 Huigu 1st East Road Tianfu International Bio-Town, Shuangliu District, Chengdu 610200 Sichuan China
| | - Jason S. Chen
- Automated Synthesis FacilityThe Scripps Research Institute 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Phil S. Baran
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Philip E. Dawson
- Department of ChemistryScripps Research 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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123
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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124
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Song M, Hwang GT. DNA-Encoded Library Screening as Core Platform Technology in Drug Discovery: Its Synthetic Method Development and Applications in DEL Synthesis. J Med Chem 2020; 63:6578-6599. [PMID: 32039601 DOI: 10.1021/acs.jmedchem.9b01782] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library technology (DELT) was introduced to our medicinal chemistry society more than 20 years ago. The application of DELT in the development of clinical candidates has been actively reported in the literature recently. A few representative examples include RIP1K inhibitors for inflammatory diseases and sEH inhibitors for endothelial dysfunction or abnormal tissue repair, among many others. Here, the authors would like to recall the recent developments in on-DNA synthetic methodologies for DEL construction and to analyze recent examples in the literature of DELT-based drug development efforts pursued in both the academic and industrial sectors. With this perspective, we hope to provide a useful summary of recent DELT-based drug discovery research and to discuss the future scope of DELT in medicinal chemistry.
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Affiliation(s)
- Minsoo Song
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Cheombok-ro, Dong-gu, Daegu 41061, Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea
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125
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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126
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Su L, Feng J, Peng T, Wan J, Fan J, Li J, O’Connell J, Lancia DR, Franklin GJ, Liu G. Synthesis of Multifunctional 2-Aminobenzimidazoles on DNA via Iodine-Promoted Cyclization. Org Lett 2020; 22:1290-1294. [DOI: 10.1021/acs.orglett.9b04578] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liqiang Su
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Feng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Ting Peng
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jing Fan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
| | - Jonathan O’Connell
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - David R. Lancia
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - G. Joseph Franklin
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, People’s Republic of China
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127
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Hackler AL, FitzGerald FG, Dang VQ, Satz AL, Paegel BM. Off-DNA DNA-Encoded Library Affinity Screening. ACS COMBINATORIAL SCIENCE 2020; 22:25-34. [PMID: 31829554 DOI: 10.1021/acscombsci.9b00153] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-encoded library (DEL) technology is emerging as a key element of the small molecule discovery toolbox. Conventional DEL screens (i.e., on-DNA screening) interrogate large combinatorial libraries via affinity selection of DNA-tagged library members that are ligands of a purified and immobilized protein target. In these selections, the DNA tags can materially and undesirably influence target binding and, therefore, the experiment outcome. Here, we use a solid-phase DEL and droplet-based microfluidic screening to separate the DEL member from its DNA tag (i.e., off-DNA screening), for subsequent in-droplet laser-induced fluorescence polarization (FP) detection of target binding, obviating DNA tag interference. Using the receptor tyrosine kinase (RTK) discoidin domain receptor 1 (DDR1) as a proof-of-concept target in a droplet-scale competition-binding assay, we screened a 67 100-member solid-phase DEL of drug-like small molecules for competitive ligands of DDR1 and identified several known RTK inhibitor pharmacophores, including azaindole- and quinazolinone-containing monomers. Off-DNA DEL affinity screening with FP detection is potentially amenable to a wide array of target classes, including nucleic acid binding proteins, proteins that are difficult to overexpress and purify, or targets with no known activity assay.
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Affiliation(s)
| | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel Hoffman-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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128
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Schneider P, Walters WP, Plowright AT, Sieroka N, Listgarten J, Goodnow RA, Fisher J, Jansen JM, Duca JS, Rush TS, Zentgraf M, Hill JE, Krutoholow E, Kohler M, Blaney J, Funatsu K, Luebkemann C, Schneider G. Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov 2019. [DOI: 78495111110.1038/s41573-019-0050-3' target='_blank'>'"<>78495111110.1038/s41573-019-0050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [78495111110.1038/s41573-019-0050-3','', '10.1021/acs.jmedchem.5b01874')">Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
78495111110.1038/s41573-019-0050-3" />
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129
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Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov 2019; 19:353-364. [DOI: 10.1038/s41573-019-0050-3] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2019] [Indexed: 12/17/2022]
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130
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Liu W, Deng W, Sun S, Yu C, Su X, Wu A, Yuan Y, Ma Z, Li K, Yang H, Peng X, Dietrich J. A Strategy for the Synthesis of Sulfonamides on DNA. Org Lett 2019; 21:9909-9913. [DOI: 10.1021/acs.orglett.9b03843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wei Liu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Wei Deng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Saisai Sun
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Chunyan Yu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xubo Su
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Aliang Wu
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Youlang Yuan
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Zhonglin Ma
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Ke Li
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Hongfang Yang
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Xuanjia Peng
- WuXi AppTec (Shanghai) Co., Ltd. 288 Middle Fu Te Road, Shanghai 200131, China
| | - Justin Dietrich
- Research and Development, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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131
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Gironda-Martínez A, Neri D, Samain F, Donckele EJ. DNA-Compatible Diazo-Transfer Reaction in Aqueous Media Suitable for DNA-Encoded Chemical Library Synthesis. Org Lett 2019; 21:9555-9558. [DOI: 10.1021/acs.orglett.9b03726] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
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132
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Zhu H, Flanagan ME, Stanton RV. Designing DNA Encoded Libraries of Diverse Products in a Focused Property Space. J Chem Inf Model 2019; 59:4645-4653. [DOI: 10.1021/acs.jcim.9b00729] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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133
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Geigle SN, Petersen AC, Satz AL. Development of DNA-Compatible Van Leusen Three-Component Imidazole Synthesis. Org Lett 2019; 21:9001-9004. [DOI: 10.1021/acs.orglett.9b03406] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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134
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Kunig VBK, Ehrt C, Dömling A, Brunschweiger A. Isocyanide Multicomponent Reactions on Solid-Phase-Coupled DNA Oligonucleotides for Encoded Library Synthesis. Org Lett 2019; 21:7238-7243. [PMID: 31464126 DOI: 10.1021/acs.orglett.9b02448] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isocyanide multicomponent reactions play a prominent role in drug discovery. This chemistry has hardly been investigated for compatibility with DNA-encoded combinatorial synthesis. The Ugi, Ugi-azide, and Groebke-Blackburn-Bienaymé reactions are well-tolerated by DNA on the solid phase and show a broad scope. However, an oxadiazole-forming variant of the Ugi reaction caused DNA depurination, requiring a more stable hexathymidine DNA for encoded library synthesis. Cheminformatic analysis revealed that isocyanide multicomponent-reaction-based encoded libraries cover a diverse chemical space.
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Affiliation(s)
- Verena B K Kunig
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Christiane Ehrt
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - Alexander Dömling
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Andreas Brunschweiger
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
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135
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Cai P, Yang G, Zhao L, Wan J, Li J, Liu G. Synthesis of C3-Alkylated Indoles on DNA via Indolyl Alcohol Formation Followed by Metal-Free Transfer Hydrogenation. Org Lett 2019; 21:6633-6637. [DOI: 10.1021/acs.orglett.9b02132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pinwen Cai
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guanyu Yang
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Lanzhou Zhao
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jinqiao Wan
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Jin Li
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
| | - Guansai Liu
- Discovery Chemistry Unit, HitGen Inc., Building 6, No. 8 Huigu 1st East Road, Tianfu International
Bio-Town, Shuangliu District, Chengdu 610200, Sichuan, P. R. China
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136
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Kölmel DK, Meng J, Tsai MH, Que J, Loach RP, Knauber T, Wan J, Flanagan ME. On-DNA Decarboxylative Arylation: Merging Photoredox with Nickel Catalysis in Water. ACS COMBINATORIAL SCIENCE 2019; 21:588-597. [PMID: 31283168 DOI: 10.1021/acscombsci.9b00076] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new catalytic manifold that merges photoredox with nickel catalysis in aqueous solution is presented. Specifically, the combination of a highly active, yet air-stable, nickel precatalyst with a new electron-deficient pyridyl carboxamidine ligand was key to the development of a water-compatible nickel catalysis platform, which is a crucial requirement for the preparation of DNA-encoded libraries (DELs). Together with an iridium-based photocatalyst and a powerful light source, this dual catalysis approach enabled the efficient decarboxylative arylation of α-amino acids with DNA-tagged aryl halides. This C(sp2)-C(sp3) coupling tolerates a wide variety of functional groups on both the amino acid and the aryl halide substrates. Due to the mild and DNA-compatible reaction conditions, the presented transformation holds great potential for the construction of DELs. This was further evidenced by showing that well plate-compatible LED arrays can serve as competent light sources to facilitate parallel synthesis. Lastly, we demonstrate that this procedure can serve as a blueprint toward the adaptation of other established nickel metallaphotoredox transformations to the idiosyncratic requirements of a DEL.
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Affiliation(s)
- Dominik K. Kölmel
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jiang Meng
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Mei-Hsuan Tsai
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Jiamin Que
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Richard P. Loach
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Thomas Knauber
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jinqiao Wan
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu
International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province, P. R. China
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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137
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Mabonga L, Kappo AP. Protein-protein interaction modulators: advances, successes and remaining challenges. Biophys Rev 2019; 11:559-581. [PMID: 31301019 PMCID: PMC6682198 DOI: 10.1007/s12551-019-00570-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Modulating disease-relevant protein-protein interactions (PPIs) using small-molecule inhibitors is a quite indispensable diagnostic and therapeutic strategy in averting pathophysiological cues and disease progression. Over the years, targeting intracellular PPIs as drug design targets has been a challenging task owing to their highly dynamic and expansive interfacial areas (flat, featureless and relatively large). However, advances in PPI-focused drug discovery technology have been reported and a few drugs are already on the market, with some potential drug-like candidates already in clinical trials. In this article, we review the advances, successes and remaining challenges in the application of small molecules as valuable PPI modulators in disease diagnosis and therapeutics.
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Affiliation(s)
- Lloyd Mabonga
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa.
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138
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Li JY, Miklossy G, Modukuri RK, Bohren KM, Yu Z, Palaniappan M, Faver JC, Riehle K, Matzuk MM, Simmons N. Palladium-Catalyzed Hydroxycarbonylation of (Hetero)aryl Halides for DNA-Encoded Chemical Library Synthesis. Bioconjug Chem 2019; 30:2209-2215. [PMID: 31329429 PMCID: PMC6706801 DOI: 10.1021/acs.bioconjchem.9b00447] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A strategy
for DNA-compatible, palladium-catalyzed hydroxycarbonylation
of (hetero)aryl halides on DNA–chemical conjugates has been
developed. This method generally provided the corresponding carboxylic
acids in moderate to very good conversions for (hetero)aryl iodides
and bromides, and in poor to moderate conversions for (hetero)aryl
chlorides. These conditions were further validated by application
within a DNA-encoded chemical library synthesis and subsequent discovery
of enriched features from the library in selection experiments against
two protein targets.
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Affiliation(s)
- Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Gabriella Miklossy
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Ram K Modukuri
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - John C Faver
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kevin Riehle
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
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139
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Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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140
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Flood DT, Asai S, Zhang X, Wang J, Yoon L, Adams ZC, Dillingham BC, Sanchez BB, Vantourout JC, Flanagan ME, Piotrowski DW, Richardson P, Green SA, Shenvi RA, Chen JS, Baran PS, Dawson PE. Expanding Reactivity in DNA-Encoded Library Synthesis via Reversible Binding of DNA to an Inert Quaternary Ammonium Support. J Am Chem Soc 2019; 141:9998-10006. [PMID: 31136164 PMCID: PMC7033622 DOI: 10.1021/jacs.9b03774] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA Encoded Libraries have proven immensely powerful tools for lead identification. The ability to screen billions of compounds at once has spurred increasing interest in DEL development and utilization. Although DEL provides access to libraries of unprecedented size and diversity, the idiosyncratic and hydrophilic nature of the DNA tag severely limits the scope of applicable chemistries. It is known that biomacromolecules can be reversibly, noncovalently adsorbed and eluted from solid supports, and this phenomenon has been utilized to perform synthetic modification of biomolecules in a strategy we have described as reversible adsorption to solid support (RASS). Herein, we present the adaptation of RASS for a DEL setting, which allows reactions to be performed in organic solvents at near anhydrous conditions opening previously inaccessible chemical reactivities to DEL. The RASS approach enabled the rapid development of C(sp2)-C(sp3) decarboxylative cross-couplings with broad substrate scope, an electrochemical amination (the first electrochemical synthetic transformation performed in a DEL context), and improved reductive amination conditions. The utility of these reactions was demonstrated through a DEL-rehearsal in which all newly developed chemistries were orchestrated to afford a compound rich in diverse skeletal linkages. We believe that RASS will offer expedient access to new DEL reactivities, expanded chemical space, and ultimately more drug-like libraries.
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Affiliation(s)
- Dillon T. Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shota Asai
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Xuejing Zhang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jie Wang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Leonard Yoon
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Blythe C. Dillingham
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brittany B. Sanchez
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Julien C. Vantourout
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Mark E. Flanagan
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - David W. Piotrowski
- Pfizer Medicinal Chemistry, Eastern Point Road, Groton, CT 06340, United States
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive, San Diego, CA 92121, United States
| | - Samantha A. Green
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Phil S. Baran
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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141
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Gerry CJ, Wawer MJ, Clemons PA, Schreiber SL. DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules. J Am Chem Soc 2019; 141:10225-10235. [PMID: 31184885 DOI: 10.1021/jacs.9b01203] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is challenging to incorporate stereochemical diversity and topographic complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully exploit the capabilities of modern synthetic organic chemistry. Here, we describe the design, construction, and validation of DOS-DEL-1, a library of 107 616 DNA-barcoded chiral 2,3-disubsituted azetidines and pyrrolidines. We used stereospecific C-H arylation chemistry to furnish complex scaffolds primed for DEL synthesis, and we developed an improved on-DNA Suzuki reaction to maximize library quality. We then studied both the structural diversity of the library and the physicochemical properties of individual compounds using Tanimoto multifusion similarity analysis, among other techniques. These analyses revealed not only that most DOS-DEL-1 members have "drug-like" properties, but also that the library more closely resembles compound collections derived from diversity synthesis than those from other sources (e.g., commercial vendors). Finally, we performed validation screens against horseradish peroxidase and carbonic anhydrase IX, and we developed a novel, Poisson-based statistical framework to analyze the results. A set of assay positives were successfully translated into potent carbonic anhydrase inhibitors (IC50 = 20.1-68.7 nM), which confirmed the success of the synthesis and screening procedures. These results establish a strategy to synthesize DELs with scaffold-based stereochemical diversity and complexity that does not require the development of novel DNA-compatible chemistry.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
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142
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Škopić MK, Götte K, Gramse C, Dieter M, Pospich S, Raunser S, Weberskirch R, Brunschweiger A. Micellar Brønsted Acid Mediated Synthesis of DNA-Tagged Heterocycles. J Am Chem Soc 2019; 141:10546-10555. [PMID: 31244181 DOI: 10.1021/jacs.9b05696] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The translation of well-established molecular biology methods such as genetic coding, selection, and DNA sequencing to combinatorial organic chemistry and compound identification has made extremely large compound collections, termed DNA-encoded libraries, accessible for drug screening. However, the reactivity of the DNA imposes limitations on the choice of chemical methods for encoded library synthesis. For example, strongly acidic reaction conditions must be avoided because they damage the DNA by depurination, i.e. the cleavage of purine bases from the oligomer. Application of micellar catalysis holds much promise for encoded chemistry. Aqueous micellar dispersions enabled compound synthesis under often appealingly mild conditions. Amphiphilic block copolymers covalently functionalized with sulfonic acid moieties in the lipophilic portion assemble in water and locate the Brønsted catalyst in micelles. These acid nanoreactors enabled the reaction of DNA-conjugated aldehydes to diverse substituted tetrahydroquinolines and aminoimidazopyridines by Povarov and Groebke-Blackburn-Bienaymé reactions, respectively, and the cleavage of tBoc protective groups from amines. The polymer micelle design was successfully translated to the Cu/Bipyridine/TEMPO system mediating the oxidation of DNA-coupled alcohols to the corresponding aldehydes. These results suggest a potentially broad applicability of polymer micelles for encoded chemistry.
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Affiliation(s)
- M Klika Škopić
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - K Götte
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - C Gramse
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - M Dieter
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - S Pospich
- Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 Dortmund , Germany
| | - S Raunser
- Max Planck Institute of Molecular Physiology , Otto-Hahn-Straße 11 , 44227 Dortmund , Germany
| | - R Weberskirch
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
| | - A Brunschweiger
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Straße 6 , 44227 Dortmund , Germany
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143
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Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
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144
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Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
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Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
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145
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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146
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Du HC, Bangs MC, Simmons N, Matzuk MM. Multistep Synthesis of 1,2,4-Oxadiazoles via DNA-Conjugated Aryl Nitrile Substrates. Bioconjug Chem 2019; 30:1304-1308. [PMID: 30964278 DOI: 10.1021/acs.bioconjchem.9b00188] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A multistep protocol for the synthesis of 3,5-disubstituted 1,2,4-oxadiazoles on DNA-chemical conjugates has been developed. A set of six DNA-connected aryl nitriles were converted to corresponding amidoximes with hydroxylamine followed by the O-acylation with a series of aryl and aliphatic carboxylic acids. After cyclodehydration of the O-acyl amidoximes by heating at 90 °C in pH 9.5 borate buffer for 2 h, the desired oxadiazole products were observed in 51-92% conversion with the cleavage of O-acylamidoximes as the major side-product. The reported protocol paves the way for the synthesis of oxadiazole core-focused DNA-encoded chemical libraries.
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Affiliation(s)
- Huang-Chi Du
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Madison C Bangs
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
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147
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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148
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Yuen LH, Dana S, Liu Y, Bloom SI, Thorsell AG, Neri D, Donato AJ, Kireev D, Schüler H, Franzini RM. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes. J Am Chem Soc 2019; 141:5169-5181. [DOI: 10.1021/jacs.8b08039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Srikanta Dana
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Yu Liu
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Samuel I. Bloom
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Dario Neri
- Department of Pharmaceutical Sciences, ETH Zürich, Vladimir Prelog Weg 3, 8093 Zürich, Switzerland
| | - Anthony J. Donato
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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149
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Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries. Chembiochem 2019; 20:955-962. [DOI: 10.1002/cbic.201800766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Elena Gabriele
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | | | - Sara Mulatto
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jacopo Piazzi
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
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150
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Gerry CJ, Yang Z, Stasi M, Schreiber SL. DNA-Compatible [3 + 2] Nitrone-Olefin Cycloaddition Suitable for DEL Syntheses. Org Lett 2019; 21:1325-1330. [PMID: 30762372 DOI: 10.1021/acs.orglett.9b00017] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The limited scope of DNA-compatible chemistry restricts the types of chemical features that can be incorporated into DNA-encoded libraries (DELs). Here, a method to synthesize DNA-conjugated polycyclic isoxazolidines via a [3 + 2] nitrone-olefin cycloaddition is described. The reaction is compatible with many olefin-containing substrates and diverse N-alkylhydroxylamines. The ability to perform subsequent DNA ligation and PCR amplification was also confirmed. This methodology facilitates the synthesis of DELs containing topographically complex compounds with underexplored chemical features.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Zhenhua Yang
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Michele Stasi
- Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States.,Chemical Biology and Therapeutics Science Program , Broad Institute , 415 Main Street , Cambridge , Massachusetts 02142 , United States
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