1
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Zhang P, Ye X, Wang JCK, Baddock HT, Jensvold Z, Foe IT, Loas A, Eaton DL, Hao Q, Nile AH, Pentelute BL. Reversibly Reactive Affinity Selection-Mass Spectrometry Enables Identification of Covalent Peptide Binders. J Am Chem Soc 2024; 146:15627-15639. [PMID: 38771982 DOI: 10.1021/jacs.4c05571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Covalent peptide binders have found applications as activity-based probes and as irreversible therapeutic inhibitors. Currently, there is no rapid, label-free, and tunable affinity selection platform to enrich covalent reactive peptide binders from synthetic libraries. We address this challenge by developing a reversibly reactive affinity selection platform termed ReAct-ASMS enabled by tandem high-resolution mass spectrometry (MS/MS) to identify covalent peptide binders to native protein targets. It uses mixed disulfide-containing peptides to build reversible peptide-protein conjugates that can enrich for covalent variants, which can be sequenced by MS/MS after reduction. Using this platform, we identified covalent peptide binders against two oncoproteins, human papillomavirus 16 early protein 6 (HPV16 E6) and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 protein (Pin1). The resulting peptide binders efficiently and selectively cross-link Cys58 of E6 at 37 °C and Cys113 of Pin1 at room temperature, respectively. ReAct-ASMS enables the identification of highly selective covalent peptide binders for diverse molecular targets, introducing an applicable platform to assist preclinical therapeutic development pipelines.
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Affiliation(s)
- Peiyuan Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John C K Wang
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Hannah T Baddock
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Zena Jensvold
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Ian T Foe
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dan L Eaton
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Qi Hao
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Aaron H Nile
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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2
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Jin H, Cui D, Fan Y, Li G, Zhong Z, Wang Y. Recent advances in bioaffinity strategies for preclinical and clinical drug discovery: Screening natural products, small molecules and antibodies. Drug Discov Today 2024; 29:103885. [PMID: 38278476 DOI: 10.1016/j.drudis.2024.103885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
Bioaffinity drug screening strategies have gained popularity in preclinical and clinical drug discovery for natural products, small molecules and antibodies owing to their superior selectivity, the large number of compounds to be screened and their ability to minimize the time and expenses of the drug discovery process. This paper provides a systematic summary of the principles of commonly used bioaffinity-based screening methods, elaborates on the success of bioaffinity in clinical drug development and summarizes the active compounds, preclinical drugs and marketed drugs obtained through affinity screening methods. Owing to the high demand for new drugs, bioaffinity-guided screening techniques will play a greater part in clinical drug development.
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Affiliation(s)
- Haochun Jin
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Dianxin Cui
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China
| | - Yu Fan
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China; Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China
| | - Guodong Li
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China; Zhuhai UM Science and Technology Research Institute, Zhuhai 519031, China.
| | - Zhangfeng Zhong
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
| | - Yitao Wang
- Macao Centre for Research and Development in Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
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3
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Wang G, Tan Y, Zou H, Sui X, Wang Z, Satz AL, Kuai L, Su W, Zhang Q. DNA-Compatible Cyclization Reaction to Access 1,3,4-Oxadiazoles and 1,2,4-Triazoles. Org Lett 2024; 26:1353-1357. [PMID: 38335275 DOI: 10.1021/acs.orglett.3c04240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
DNA-encoded chemical library (DECL) technology is a commonly employed screening platform in both the pharmaceutical industry and academia. To expand the chemical space of DECLs, new and robust DNA-compatible reactions are sought after. In particular, DNA-compatible cyclization reactions are highly valued, as these reactions tend to be atom economical and thus may provide lead- and drug-like molecules. Herein, we report two new methodologies employing DNA-conjugated thiosemicarbazides as a common precursor, yielding highly substituted 1,3,4-oxadiazoles and 1,2,4-triazoles. These two novel DNA-compatible reactions feature a high conversion efficiency and broad substrate scope under mild conditions that do not observably degrade DNA.
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Affiliation(s)
- Gaonan Wang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yu Tan
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hanzhi Zou
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xihang Sui
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhanlong Wang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Letian Kuai
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
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4
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Ma P, Zhang S, Huang Q, Gu Y, Zhou Z, Hou W, Yi W, Xu H. Evolution of chemistry and selection technology for DNA-encoded library. Acta Pharm Sin B 2024; 14:492-516. [PMID: 38322331 PMCID: PMC10840438 DOI: 10.1016/j.apsb.2023.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 02/08/2024] Open
Abstract
DNA-encoded chemical library (DEL) links the power of amplifiable genetics and the non-self-replicating chemical phenotypes, generating a diverse chemical world. In analogy with the biological world, the DEL world can evolve by using a chemical central dogma, wherein DNA replicates using the PCR reactions to amplify the genetic codes, DNA sequencing transcripts the genetic information, and DNA-compatible synthesis translates into chemical phenotypes. Importantly, DNA-compatible synthesis is the key to expanding the DEL chemical space. Besides, the evolution-driven selection system pushes the chemicals to evolve under the selective pressure, i.e., desired selection strategies. In this perspective, we summarized recent advances in expanding DEL synthetic toolbox and panning strategies, which will shed light on the drug discovery harnessing in vitro evolution of chemicals via DEL.
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Affiliation(s)
- Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Shuning Zhang
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qianping Huang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Zhi Zhou
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Yi
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 511436, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
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5
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Zhang J, Liu J, Li X, Ju Y, Li Y, Zhang G, Li Y. Unexpected Cyclization Product Discovery from the Photoinduced Bioconjugation Chemistry between Tetrazole and Amine. J Am Chem Soc 2024; 146:2122-2131. [PMID: 38190443 DOI: 10.1021/jacs.3c11574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Bioconjugation chemistry has emerged as a powerful tool for the modification of diverse biomolecules under mild conditions. Tetrazole, initially proposed as a bioorthogonal photoclick handle for 1,3-dipolar cyclization with alkenes, was later demonstrated to possess broader photoreactivity with carboxylic acids, serving as a versatile bioconjugation and photoaffinity labeling probe. In this study, we unexpectedly discovered and validated the photoreactivity between tetrazole and primary amine to afford a new 1,2,4-triazole cyclization product. Given the significance of functionalized N-heterocycles in medicinal chemistry, we successfully harnessed the serendipitously discovered reaction to synthesize both pharmacologically relevant DNA-encoded chemical libraries (DELs) and small molecule compounds bearing 1,2,4-triazole scaffolds. Furthermore, the mild reaction conditions and stable 1,2,4-triazole linkage found broad application in photoinduced bioconjugation scenarios, spanning from intramolecular peptide macrocyclization and templated DNA reaction cross-linking to intermolecular photoaffinity labeling of proteins. Triazole cross-linking products on lysine side chains were identified in tetrazole-labeled proteins, refining the comprehensive understanding of the photo-cross-linking profiles of tetrazole-based probes. Altogether, this tetrazole-amine bioconjugation expands the current bioconjugation toolbox and creates new possibilities at the interface of medicinal chemistry and chemical biology.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Jinlu Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yunzhu Ju
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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6
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Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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7
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Pan K, Yao Y, Zhang Y, Gu Y, Wang Y, Ma P, Hou W, Yang G, Zhang S, Xu H. Enolate-Azide [3 + 2]-Cycloaddition Reaction Suitable for DNA-Encoded Library Synthesis. Bioconjug Chem 2023; 34:1459-1466. [PMID: 37443440 DOI: 10.1021/acs.bioconjchem.3c00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The DNA-encoded chemical library (DEL) is a powerful hit selection technique in either basic science or innovative drug discovery. With the aim to circumvent the issue concerning DNA barcode damage in a conventional on-DNA copper-catalyzed azide-alkyne cycloaddition reaction (CuAAC), we have successfully developed the first DNA-compatible enolate-azide [3 + 2] cycloaddition reaction. The merits of this DEL chemistry include metal-free reaction and high DNA fidelity, high conversions and easy operation, broad substrate scope, and ready access to the highly substituted 1,4,5-trisubstituted triazoles. Thus, it will not only further enrich the DEL chemistry toolbox but also will have great potential in practical DEL synthesis.
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Affiliation(s)
- Kangyin Pan
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Ying Yao
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
| | - Wei Hou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai 201210, P. R. China
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8
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Ding Z, Wu Y, Liu L, Qi B, Peng Z. Construction of Isocytosine Scaffolds via DNA-Compatible Biginelli-like Reaction. Org Lett 2023; 25:5515-5519. [PMID: 37462924 DOI: 10.1021/acs.orglett.3c01986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Herein we report a DNA-compatible Biginelli reaction to construct isocytosine scaffolds. This reaction utilizes a one-pot reaction of DNA-conjugated guanidines with aldehydes and methyl cyanoacetates to give isocytosine derivatives, and the method is well compatible with different types of substrates. This is the first report on the synthesis of an isocytosine backbone in the field of DNA-compatible organic synthesis. The successful development of this reaction can widen the chemical space of DELs.
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Affiliation(s)
- Zhaobing Ding
- PharmaBlock Sciences (Nanjing), Inc., Nanjing 210032, Jiangsu Province, China
| | - Yizhou Wu
- PharmaBlock Sciences (Nanjing), Inc., Nanjing 210032, Jiangsu Province, China
| | - Liu Liu
- PharmaBlock Sciences (Nanjing), Inc., Nanjing 210032, Jiangsu Province, China
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9
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Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
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Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
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10
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Nie Q, Sun J, Fang X, He X, Xiong F, Zhang G, Li Y, Li Y. Antimony salt-promoted cyclization facilitating on-DNA syntheses of dihydroquinazolinone derivatives and its applications. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Xiong F, Xu H, Yu M, Chen X, Zhong Z, Guo Y, Chen M, Ou H, Wu J, Xie A, Xiong J, Xu L, Zhang L, Zhong Q, Huang L, Li Z, Zhang T, Jin F, He X. 3CLpro inhibitors: DEL-based molecular generation. Front Pharmacol 2022; 13:1085665. [PMID: 36569316 PMCID: PMC9768338 DOI: 10.3389/fphar.2022.1085665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Molecular generation (MG) via machine learning (ML) has speeded drug structural optimization, especially for targets with a large amount of reported bioactivity data. However, molecular generation for structural optimization is often powerless for new targets. DNA-encoded library (DEL) can generate systematic, target-specific activity data, including novel targets with few or unknown activity data. Therefore, this study aims to overcome the limitation of molecular generation in the structural optimization for the new target. Firstly, we generated molecules using the structure-affinity data (2.96 million samples) for 3C-like protease (3CLpro) from our own-built DEL platform to get rid of using public databases (e.g., CHEMBL and ZINC). Subsequently, to analyze the effect of transfer learning on the positive rate of the molecule generation model, molecular docking and affinity model based on DEL data were applied to explore the enhanced impact of transfer learning on molecule generation. In addition, the generated molecules are subjected to multiple filtering, including physicochemical properties, drug-like properties, and pharmacophore evaluation, molecular docking to determine the molecules for further study and verified by molecular dynamics simulation.
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Affiliation(s)
- Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
| | - Honggui Xu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Mingao Yu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Xingyu Chen
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Zhenmin Zhong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Yuhan Guo
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Meihong Chen
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Huanfang Ou
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Jiaqi Wu
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Anhua Xie
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Jiaqi Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Linlin Xu
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Lanmei Zhang
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Qijian Zhong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Liye Huang
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | - Zhenwei Li
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China
| | | | - Feng Jin
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
| | - Xun He
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen, China,*Correspondence: Feng Xiong, ; Feng Jin, ; Xun He,
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12
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Li X, Zhang J, Liu C, Sun J, Li Y, Zhang G, Li Y. Aryl diazonium intermediates enable mild DNA-compatible C-C bond formation for medicinally relevant combinatorial library synthesis. Chem Sci 2022; 13:13100-13109. [PMID: 36425486 PMCID: PMC9667928 DOI: 10.1039/d2sc04482j] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/24/2022] [Indexed: 08/24/2023] Open
Abstract
Forging carbon-carbon (C-C) linkage in DNA-encoded combinatorial library synthesis represents a fundamental task for drug discovery, especially with broad substrate scope and exquisite functional group tolerance. Here we reported the palladium-catalyzed Suzuki-Miyaura, Heck and Hiyama type cross-coupling via DNA-conjugated aryl diazonium intermediates for DNA-encoded chemical library (DEL) synthesis. Starting from commodity arylamines, this synthetic route facilely delivers vast chemical diversity at a mild temperature and pH, thus circumventing damage to fragile functional groups. Given its orthogonality with traditional aryl halide-based cross-coupling, the aryl diazonium-centered strategy expands the compatible synthesis of complex C-C bond-connected scaffolds. In addition, DNA-tethered pharmaceutical compounds (e.g., HDAC inhibitor) are constructed without decomposition of susceptible bioactive warheads (e.g., hydroxamic acid), emphasizing the superiority of the aryl diazonium-based approach. Together with the convenient transformation into an aryl azide photo-crosslinker, aryl diazonium's DNA-compatible diversification synergistically demonstrated its competence to create medicinally relevant combinatorial libraries and investigate protein-ligand interactions in pharmaceutical research.
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Affiliation(s)
- Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Changyang Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University 401331 Chongqing P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University P. R. China
- Beijing National Laboratory for Molecular Sciences Beijing 100190 P. R. China
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13
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Gao Y, Sun Y, Zhao G, Zhang G, Li Y, Li Y. On-DNA Synthesis of Functionalized 4 H-Pyran Scaffolds for Focused DNA-Encoded Chemical Libraries. Org Lett 2022; 24:6664-6669. [PMID: 36053053 DOI: 10.1021/acs.orglett.2c02714] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionalized 4H-pyran scaffold has aroused synthetic attention because it is widely found in many interesting pharmacologically relevant compounds. We here disclose its incorporation into DNA-encoded chemical libraries, combining this scaffold with the merits of scaffold architecture in drug design. Under the optimized DNA-compatible conditions, functionalized 4H-pyrans were efficiently formed with a broad substrate scope. Among the 4H-pyrans formed, the axial structure features rotational restriction, and the spirocyclic structure provides rigidity and three-dimensionality. These efforts open the door for the construction of DNA-encoded chemical libraries with more consideration for this structural architecture.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China.,Beijing National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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14
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Xu H, Tan T, Zhang Y, Wang Y, Pan K, Yao Y, Zhang S, Gu Y, Chen W, Li J, Dong H, Meng Y, Ma P, Hou W, Yang G. Metal-Free and Open-Air Arylation Reactions of Diaryliodonium Salts for DNA-Encoded Library Synthesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202790. [PMID: 35853237 PMCID: PMC9475524 DOI: 10.1002/advs.202202790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
A successful DNA-encoded library (DEL) will consist of diverse skeletons and cover chemical space as comprehensive as possible to fully realize its potential in drug discovery and chemical biology. However, the lack of versatile on-DNA arylation methods for phenols that are less nucleophilic and reactive poses a great hurdle for DEL to include diaryl ether, a privileged chemotype in pharmaceuticals and natural products. This work describes the use of "substrate activation" approach to address the arylation of DNA-conjugated phenols. Diaryliodonium salt, a highly electrophilic and reactive arylation reagent, is employed as Ar+ sources to ensure highly selective on-DNA arylation of phenols and oximes with both high yields and DNA fidelity. Notably, the new on-DNA arylation reaction can be applied to the late-stage modification of peptides containing tyrosine side-chain and to synthesize DNA-tagged analogues of existing drug molecules such as sorafenib, a known pan-kinase inhibitor. The new on-DNA diaryliodonium salts chemistry affords a greater flexibility in DEL design and synthesis.
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Affiliation(s)
- Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yiyuan Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yan Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Kangyin Pan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Ying Yao
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
| | - Hewei Dong
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Yu Meng
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
- Shanghai Key Laboratory of Orthopedic ImplantsDepartment of Orthopedic SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong UniversitySchool of MedicineShanghai200011P. R. China
| | - Wei Hou
- College of Pharmaceutical Science and Institute of Drug Development & Chemical BiologyZhejiang University of TechnologyHangzhou310014P. R. China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210P. R. China
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15
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Cui M, Zhao X, Reddavide FV, Gaillez MP, Heiden S, Mannocci L, Thompson M, Zhang Y. Nonlinear manipulation and analysis of large DNA datasets. Nucleic Acids Res 2022; 50:8974-8985. [PMID: 35947747 PMCID: PMC9410889 DOI: 10.1093/nar/gkac672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 06/18/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Information processing functions are essential for organisms to perceive and react to their complex environment, and for humans to analyze and rationalize them. While our brain is extraordinary at processing complex information, winner-take-all, as a type of biased competition is one of the simplest models of lateral inhibition and competition among biological neurons. It has been implemented as DNA-based neural networks, for example, to mimic pattern recognition. However, the utility of DNA-based computation in information processing for real biotechnological applications remains to be demonstrated. In this paper, a biased competition method for nonlinear manipulation and analysis of mixtures of DNA sequences was developed. Unlike conventional biological experiments, selected species were not directly subjected to analysis. Instead, parallel computation among a myriad of different DNA sequences was carried out to reduce the information entropy. The method could be used for various oligonucleotide-encoded libraries, as we have demonstrated its application in decoding and data analysis for selection experiments with DNA-encoded chemical libraries against protein targets.
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Affiliation(s)
| | | | | | - Michelle Patino Gaillez
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | | | | | - Yixin Zhang
- To whom correspondence should be addressed. Tel: +49 351 463 43040;
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16
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Sun J, Nie Q, Fang X, He Z, Zhang G, Li Y, Li Y. Vinyl azide as a synthon for DNA-compatible divergent transformations into N-heterocycles. Org Biomol Chem 2022; 20:5045-5049. [PMID: 35703385 DOI: 10.1039/d2ob00862a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Inspired by diversity-oriented synthesis, we have developed a series of DNA-compatible transformations utilizing on-DNA vinyl azide as a synthon to forge divergent N-heterocyclic scaffolds. Polysubstituted imidazoles and isoquinolines were efficiently obtained with moderate-to-excellent conversions. Besides, the "one-pot" strategy to prepare in-house on-DNA vinyl azides afforded synthons readily. Results from substrate scope exploration and enzymatic ligation further demonstrate the feasibility of these N-heterocycle syntheses in DNA-encoded chemical library construction.
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Affiliation(s)
- Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Zhiwei He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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17
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Siripuram VK, Sunkari YK, Nguyen TL, Flajolet M. DNA-Compatible Suzuki-Miyaura Cross-Coupling Reaction of Aryl Iodides With (Hetero)Aryl Boronic Acids for DNA-Encoded Libraries. Front Chem 2022; 10:894603. [PMID: 35774858 PMCID: PMC9237475 DOI: 10.3389/fchem.2022.894603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
An efficient method for the C-C bond formation via water soluble Na2PdCl4/sSPhos mediated Suzuki-Miyaura cross-coupling reaction of DNA-conjugated aryl iodide with (het)aryl boronic acids has been developed. This reaction proceeds at 37°C in water and acetonitrile (4:1) system. We also demonstrated that numerous aromatic and heteroaromatic boronic acids of different electronic natures, and harboring various functional groups, were highly compatible providing the desired coupling products in good to excellent yields. This DNA-compatible Suzuki-Miyaura cross-coupling reaction has strong potential to construct DNA-Encoded Libraries (DELs) in the context of drug discovery.
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Affiliation(s)
| | | | | | - Marc Flajolet
- *Correspondence: Vijay Kumar Siripuram, ; Marc Flajolet,
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18
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Fang X, Wang Y, He P, Liao H, Zhang G, Li Y, Li Y. Visible Light-Promoted Divergent Benzoheterocyclization from Aldehydes for DNA-Encoded Chemical Libraries. Org Lett 2022; 24:3291-3296. [PMID: 35467894 DOI: 10.1021/acs.orglett.2c01187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Benzoheterocyclics have been widely adopted as drug-like core scaffolds that can be incorporated into DNA-encoded chemical library technology for high-throughput hit discovery. Here, we present a visible light-promoted divergent synthesis of on-DNA benzoheterocycles from aldehydes. Four types of DNA-conjugated benzoheterocyclics were obtained under mild conditions with a broad substrate scope. A cross substrate scope study, together with enzymatic ligation and subsequent chemical diversifications, were conducted, demonstrating the feasibility of this approach in DNA-encoded chemical library construction.
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Affiliation(s)
- Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Pengyang He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Huilin Liao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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19
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Kojima E, Iimuro A, Nakajima M, Kinuta H, Asada N, Sako Y, Nakata Z, Uemura K, Arita S, Miki S, Wakasa-Morimoto C, Tachibana Y. Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template. J Med Chem 2022; 65:6157-6170. [PMID: 35416651 DOI: 10.1021/acs.jmedchem.1c02217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel strategy for lead identification that we have dubbed the "Pocket-to-Lead" strategy is demonstrated using HIV-1 protease as a model target. Sometimes, it is difficult to obtain hit compounds because of the difficulties in satisfying the complex pharmacophoric features. In this study, a virtual fragment hit which does not match all of the pharmacophore features but has key interactions and vectors that could grow into remaining pharmacophore features was optimized in silico. The designed compound 9 demonstrated weak but evident inhibitory activity (IC50 = 54 μM), and the design concept was proven by the co-crystal structure. Then, structure-based drug design promptly gave compound 14 (IC50 = 0.0071 μM, EC50 = 0.86 μM), an almost 10,000-fold improvement in activity from 9. The structure of the designed molecules proved to be novel with high synthetic feasibility, indicating the usefulness of this strategy to tackle tough targets with complex pharmacophore.
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Affiliation(s)
- Eiichi Kojima
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsuhiro Iimuro
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Mado Nakajima
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hirotaka Kinuta
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Naoya Asada
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Sako
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Zenzaburo Nakata
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Kentaro Uemura
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shuhei Arita
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shinobu Miki
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Chiaki Wakasa-Morimoto
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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20
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Li Y, Zhao G, Fan X, Li Y, Zhang G. Switchable DNA-Encoded Chemical Library: Interconversion between Double- and Single-Stranded DNA Formats. Chembiochem 2022; 23:e202200025. [PMID: 35352452 DOI: 10.1002/cbic.202200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/10/2022] [Indexed: 11/07/2022]
Abstract
DNA-Encoded Chemical Library (DEL) has attracted substantial attention due to the infinite possibility for hit discovery in both pharmaceutical companies and academia. The encoding method is the initial step of DEL construction and one of the cornerstones of DEL applications. Classified by the DNA format, the existing DEL encoding strategies could be categorized into single-stranded DNA-based strategies and double-stranded DNA-based strategies. The two DEL formats have their unique advantages but are usually incompatible with each other. To address this issue, we proposed the concept of interconversion between double- and single-stranded DEL based on the "reversible covalent headpiece (RCHP)" design, which combined maximum robustness of synthesis with extraordinary flexibility of applications in distinct setups. Future opportunities in this field were also proposed to advance DEL technology to a comprehensive drug discovery platform.
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Affiliation(s)
- Yizhou Li
- Chongqing University, School of Pharmaceutical Sciences, Chongqing College Town, Shapingba, 401331, Chongqing, CHINA
| | - Guixian Zhao
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Xiaohong Fan
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Yangfeng Li
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Gong Zhang
- Chongqing University, School of Pharmaceutical Science, CHINA
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21
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Yang S, Zhao G, Gao Y, Sun Y, Zhang G, Fan X, Li Y, Li Y. In-solution direct oxidative coupling for the integration of sulfur/selenium into DNA-encoded chemical libraries. Chem Sci 2022; 13:2604-2613. [PMID: 35340849 PMCID: PMC8890091 DOI: 10.1039/d1sc06268a] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/29/2022] [Indexed: 12/27/2022] Open
Abstract
Sulfur/selenium-containing electron-rich arenes (ERAs) exist in a wide range of both approved and investigational drugs with diverse pharmacological activities. These unique chemical structures and bioactive properties, if combined with the emerging DNA-encoded chemical library (DEL) technique, would facilitate drug and chemical probe discovery. However, it remains challenging, as there is no general DNA-compatible synthetic methodology available for the formation of C–S and C–Se bonds in aqueous solution. Herein, an in-solution direct oxidative coupling procedure that could efficiently integrate sulfur/selenium into the ERA under mild conditions is presented. This method features simple DNA-conjugated electron-rich arenes with a broad substrate scope and a transition-metal free process. Furthermore, this synthetic methodology, examined by a scale-up reaction test and late-stage precise modification in a mock peptide-like DEL synthesis, will enable its utility for the synthesis of sulfur/selenium-containing DNA-encoded libraries and the discovery of bioactive agents. DNA-compatible direct oxidative coupling using various sulfur/selenium sources has been achieved, featuring pre-functionalization-free substrates and transition metal-free condition.![]()
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Affiliation(s)
- Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Xiaohong Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China .,Pharmaceutical Department of Chongqing Three Gorges Central Hospital, Chongqing University Chongqing 404100 P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University Chongqing 401331 P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University Chongqing 400044 P. R. China
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22
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Ge R, Shen Z, Yin J, Chen W, Zhang Q, An Y, Tang D, Satz AL, Su W, Kuai L. Discovery of SARS-CoV-2 main protease covalent inhibitors from a DNA-encoded library selection. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:79-85. [PMID: 35063690 PMCID: PMC8767972 DOI: 10.1016/j.slasd.2022.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent inhibitors targeting the main protease (Mpro, or 3CLpro) of SARS-CoV-2 have shown promise in preclinical investigations. Herein, we report the discovery of two new series of molecules that irreversibly bind to SARS-CoV-2 Mpro. These acrylamide containing molecules were discovered using our covalent DNA-encoded library (DEL) screening platform. Following selection against SARS-CoV-2 Mpro, off-DNA compounds were synthesized and investigated to determine their inhibitory effects, the nature of their binding, and to generate preliminary structure-activity relationships. LC-MS analysis indicates a 1:1 (covalent) binding stoichiometry between our hit molecules and SARS-CoV-2 Mpro. Fluorescent staining assay for covalent binding in the presence of cell lysate suggests reasonable selectivity for SARS-CoV-2 Mpro. And lastly, inhibition of enzymatic activity was also observed against a panel of 3CLpro enzymes from different coronavirus strains, with IC50 values ranging from inactive to single digit micromolar. Our results indicate that DEL selection is a useful approach for identifying covalent inhibitors of cysteine proteases.
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Affiliation(s)
- Rui Ge
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zuyuan Shen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Yin
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenhua Chen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Dewei Tang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Letian Kuai
- WuXi AppTec(,) 55 Cambridge Parkway, 8th Floor(,) Cambridge, MA 02142, USA.
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23
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Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double‐ and Single‐Stranded DNA‐Encoded Chemical Libraries. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research Innovative Drug Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Chemical Biology Research Center School of Pharmaceutical Sciences Chongqing University Chongqing 401331 P. R. China
- Key Laboratory of Biorheological Science and Technology Ministry of Education College of Bioengineering Chongqing University 400044 Chongqing P. R. China
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24
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Zhong S, Fang X, Wang Y, Zhang G, Li Y, Li Y. DNA-Compatible Diversification of Indole π-Activated Alcohols via a Direct Dehydrative Coupling Strategy. Org Lett 2022; 24:1022-1026. [PMID: 35050627 DOI: 10.1021/acs.orglett.1c04169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Indole-based diversification is highly desired in the DNA-encoded chemical library construction. Herein, we present a general strategy for on-DNA synthesis of diverse C3-functionalized indole derivatives via indole π-activated alcohol formation followed by direct dehydrative coupling. Highly efficient bond linkages of C-C, C-N, and C-S were achieved to fuse building blocks that are widely commercially available. DNA-encoding compatibility of the method has been further demonstrated to pave an avenue for application in constructing indole-focused three-dimensional libraries.
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Affiliation(s)
- Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yiting Wang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, P. R. China
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25
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Nie Q, Fang X, Liu C, Zhang G, Fan X, Li Y, Li Y. DNA-Compatible ortho-Phthalaldehyde (OPA)-Mediated 2-Substituted Isoindole Core Formation and Applications. J Org Chem 2022; 87:2551-2558. [DOI: 10.1021/acs.joc.1c02496] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
| | - Changyang Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
| | - Xiaohong Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
- Pharmaceutical Department of Chongqing Three Gorges Central Hospital, Chongqing University Three Gorges Hospital, Chongqing 404100, People’s Republic of China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, People’s Republic of China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, People’s Republic of China
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26
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Gao Y, Zhao G, He P, Zhang G, Li Y, Li Y. DNA-Compatible Synthesis of α,β-Epoxyketones for DNA-Encoded Chemical Libraries. Bioconjug Chem 2022; 33:105-110. [PMID: 34927428 DOI: 10.1021/acs.bioconjchem.1c00567] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As a powerful platform in drug discovery, the DNA-encoded chemical library technique enables the generation of numerous chemical members with high structural diversity. Epoxides widely exist in a variety of approved drugs and clinical candidates, eliciting multiple pharmaceutical activities. Herein, we report a non-oxidative DNA-compatible synthesis of di-/trisubstituted α,β-epoxyketones by implementing aldehydes and α-chlorinated ketones as abundant building blocks. This methodology was demonstrated to cover a broad substrate scope with medium-to-excellent conversions. Further structural diversification and transformation were also successfully explored to fully leverage α,β-epoxyketone moiety.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Pengyang He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331, Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044, Chongqing, P. R. China
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27
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Cai B, Krusemark CJ. Multiplexed Small‐Molecule‐Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113515] [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]
Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Center for Cancer Research Purdue University West Lafayette IN 47907 USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology Purdue Center for Cancer Research Purdue University West Lafayette IN 47907 USA
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28
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Cai B, Krusemark CJ. Multiplexed Small-Molecule-Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis. Angew Chem Int Ed Engl 2022; 61:e202113515. [PMID: 34758183 PMCID: PMC8748404 DOI: 10.1002/anie.202113515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/04/2021] [Indexed: 01/19/2023]
Abstract
Small-molecule binding assays to target proteins are a core component of drug discovery and development. While a number of assay formats are available, significant drawbacks still remain in cost, sensitivity, and throughput. To improve assays by capitalizing on the power of DNA sequence analysis, we have developed an assay method that combines DNA encoding with split-and-pool sample handling. The approach involves affinity labeling of DNA-linked ligands to a protein target. Critically, the labeling event assesses ligand binding and enables subsequent pooling of several samples. Application of a purifying selection on the pool for protein-labeled DNAs allows detection of ligand binding by quantification of DNA barcodes. We demonstrate the approach in both ligand displacement and direct binding formats and demonstrate its utility in determination of relative ligand affinity, profiling ligand specificity, and high-throughput small-molecule screening.
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Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
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29
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Ma F, Li J, Zhang S, Gu Y, Tan T, Chen W, Wang S, Xu H, Yang G, Lerner RA. Metal-Catalyzed One-Pot On-DNA Syntheses of Diarylmethane and Thioether Derivatives. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05338] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Fei Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Jie Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Shuning Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yuang Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Tingting Tan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Wanting Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Shuyue Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Richard A. Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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30
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Shi EX. High-Throughput Binder Confirmation Using Affinity Selection Mass Spectrometry. Methods Mol Biol 2022; 2541:215-223. [PMID: 36083560 DOI: 10.1007/978-1-0716-2545-3_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Affinity selection mass spectrometry (AS-MS) was recently applied to a new high-throughput binder confirmation (HTBC) platform. The HTBC-AS-MS platform can assess target engagement for hundreds of chemical series per target and is used at GSK to prioritize synthesis decisions for follow-up organic synthesis of DNA-encoded library technology (ELT) hits.
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Affiliation(s)
- Eric X Shi
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
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31
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Gao Y, Sun Y, Fang X, Zhao G, Li X, Zhang G, Li Y, Li Y. Development of on-DNA vinyl sulfone synthesis for DNA-encoded chemical libraries. Org Chem Front 2022. [DOI: 10.1039/d2qo00881e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present the development of an efficient synthetic route to generate a DNA-compatible vinyl sulfone functional group, and the subsequent chemical transformations demonstrated the feasibility of our method in DEL construction.
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Affiliation(s)
- Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yang Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Xufeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China
- Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
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32
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Zhao G, Zhong S, Zhang G, Li Y, Li Y. Reversible Covalent Headpiece Enables Interconversion between Double- and Single-Stranded DNA-Encoded Chemical Libraries. Angew Chem Int Ed Engl 2021; 61:e202115157. [PMID: 34904335 DOI: 10.1002/anie.202115157] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The use of a proper encoding methodology is one of the most important aspects when practicing DEL technology. A "headpiece"-based double-stranded DEL encoding method is currently the most widely used for productive DEL. However, the robustness of double-stranded DEL construction conflicts with the versatility presented by single-stranded DEL applications. We here report a novel encoding method, which is based on a "reversible covalent headpiece (RCHP)". The RCHP allows reversible interconversion between double- and single-stranded DNA formats, providing an avenue to robust synthesis and allowing for the applications in distinct setups. We have validated the versatility of this encoding method with encoded self-assembled chemical library and DNA-encoded dynamic library technology. Notably, based on the RCHP-settled library construction, a unique "ternary covalent complex" mediating ligand isolation methodology against non-immobilized targets was developed.
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Affiliation(s)
- Guixian Zhao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Shuting Zhong
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044, Chongqing, P. R. China
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33
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Düzgüneş N, Fernandez-Fuentes N, Konopka K. Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design. Pathogens 2021; 10:1599. [PMID: 34959554 PMCID: PMC8709411 DOI: 10.3390/pathogens10121599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a "six-helix bundle" after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.
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Affiliation(s)
- Nejat Düzgüneş
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK;
| | - Krystyna Konopka
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
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34
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Zhang J, Li X, Wei H, Li Y, Zhang G, Li Y. Sequential DNA-Encoded Building Block Fusion for the Construction of Polysubstituted Pyrazoline Core Libraries. Org Lett 2021; 23:8429-8433. [PMID: 34652930 DOI: 10.1021/acs.orglett.1c03145] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The construction of chemical libraries containing polysubstituted pyrazoline scaffolds is highly desirable for the discovery of novel chemical ligands for biological targets. Herein, we report a sequential DNA-encoded synthesis strategy for polysubstituted pyrazoline heterocycles, which fuses a broad panel of aldehydes, aryl amines, and alkenes as building blocks. Furthermore, mock library synthesis and selection demonstrated the ability of the method to produce DNA-encoded focused libraries with highly functionalized pyrazoline cores.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Xianfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Haimei Wei
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, P. R. China
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35
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Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.09.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Abstract
INTRODUCTION Undruggable targets refer to clinically meaningful therapeutic targets that are 'difficult to drug' or 'yet to be drugged' via traditional approaches. Featuring characteristics of lacking defined ligand-binding pockets, non-catalytic protein-protein interaction functional modes and less-investigated 3D structures, these undruggable targets have been targeted with novel therapeutic entities developed with the progress of unconventional drug discovery approaches, such as targeted degradation molecules and display technologies. AREA COVERED This review first presents the concept of 'undruggable' exemplified by RAS and other targets. Next, detailed strategies are illustrated in two aspects: innovation of therapeutic entities and development of unconventional drug discovery technologies. Finally, case studies covering typical undruggable targets (Bcl-2, p53, and RAS) are depicted to further demonstrate the feasibility of the strategies and entities above. EXPERT OPINION Targeting the undruggable expands the scope of therapeutically reachable targets. Consequently, it represents the drug discovery frontier. Biomedical studies are capable of dissecting disease mechanisms, thus broadening the list of undruggable targets. Encouraged by the recent approval of the KRAS inhibitor Sotorasib, we believe that merging multiple discovery approaches and exploiting various novel therapeutic entities would pave the way for dealing with more 'undruggable' targets in the future.
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Affiliation(s)
- Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yuting Gao
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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37
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Klika Škopić M, Gramse C, Oliva R, Pospich S, Neukirch L, Manisegaran M, Raunser S, Winter R, Weberskirch R, Brunschweiger A. Towards DNA-Encoded Micellar Chemistry: DNA-Micelle Association and Environment Sensitivity of Catalysis. Chemistry 2021; 27:10048-10057. [PMID: 33979454 PMCID: PMC8361662 DOI: 10.1002/chem.202100980] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Indexed: 02/06/2023]
Abstract
The development of DNA-compatible reaction methodologies is a central theme to advance DNA-encoded screening library technology. Recently, we were able to show that sulfonic acid-functionalized block copolymer micelles facilitated Brønsted acid-promoted reactions such as the Povarov reaction on DNA-coupled starting materials with minimal DNA degradation. Here, the impact of polymer composition on micelle shape, and reaction conversion was investigated. A dozen sulfonic acid-functionalized block copolymers of different molar mass and composition were prepared by RAFT polymerization and were tested in the Povarov reaction, removal of the Boc protective group, and the Biginelli reaction. The results showed trends in the polymer structure-micellar catalytic activity relationship. For instance, micelles composed of block copolymers with shorter acrylate ester chains formed smaller particles and tended to provide faster reaction kinetics. Moreover, fluorescence quenching experiments as well as circular dichroism spectroscopy showed that DNA-oligomer-conjugates, although highly water-soluble, accumulated very effectively in the micellar compartments, which is a prerequisite for carrying out a DNA-encoded reaction in the presence of polymer micelles.
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Affiliation(s)
- Mateja Klika Škopić
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Christian Gramse
- Polymer Hybrid SystemsFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Rosario Oliva
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Sabrina Pospich
- Department of Structural BiochemistryMax Planck Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
| | - Laura Neukirch
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Magiliny Manisegaran
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Stefan Raunser
- Department of Structural BiochemistryMax Planck Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
| | - Roland Winter
- Physical Chemistry – Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 4a44227DortmundGermany
| | - Ralf Weberskirch
- Polymer Hybrid SystemsFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
| | - Andreas Brunschweiger
- Medicinal ChemistryFaculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn-Straße 644227DortmundGermany
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38
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Favalli N, Bassi G, Pellegrino C, Millul J, De Luca R, Cazzamalli S, Yang S, Trenner A, Mozaffari NL, Myburgh R, Moroglu M, Conway SJ, Sartori AA, Manz MG, Lerner RA, Vogt PK, Scheuermann J, Neri D. Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications. Nat Chem 2021; 13:540-548. [PMID: 33833446 PMCID: PMC8405038 DOI: 10.1038/s41557-021-00660-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023]
Abstract
The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting.
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Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Christian Pellegrino
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Su Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA
| | - Peter K Vogt
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
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39
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Su W, Ge R, Ding D, Chen W, Wang W, Yan H, Wang W, Yuan Y, Liu H, Zhang M, Zhang J, Shu Q, Satz AL, Kuai L. Triaging of DNA-Encoded Library Selection Results by High-Throughput Resynthesis of DNA-Conjugate and Affinity Selection Mass Spectrometry. Bioconjug Chem 2021; 32:1001-1007. [PMID: 33914520 DOI: 10.1021/acs.bioconjchem.1c00170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
DNA encoded library (DEL) technology allows for rapid identification of novel small-molecule ligands and thus enables early-stage drug discovery. DEL technology is well-established, numerous cases of discovered hit molecules have been published, and the technology is widely employed throughout the pharmaceutical industry. Nonetheless, DEL selection results can be difficult to interpret, as library member enrichment may derive from not only desired products, but also DNA-conjugated byproducts and starting materials. Note that DELs are generally produced using split-and-pool combinatorial chemistry, and DNA-conjugated byproducts and starting materials cannot be removed from the library mixture. Herein, we describe a method for high-throughput parallel resynthesis of DNA-conjugated molecules such that byproducts, starting materials, and desired products are produced in a single pot, using the same chemical reactions and reagents as during library production. The low-complexity mixtures of DNA-conjugate are then assessed for protein binding by affinity selection mass spectrometry and the molecular weights of the binding ligands ascertained. This workflow is demonstrated to be a practical tool to triage and validate potential hits from DEL selection data.
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Affiliation(s)
- Wenji Su
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Rui Ge
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Duanchen Ding
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Wenhua Chen
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Wenqing Wang
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Hao Yan
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Weikun Wang
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Youlang Yuan
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Huan Liu
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Meng Zhang
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Jiyuan Zhang
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Qisheng Shu
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Alexander L Satz
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec (Shanghai) Co., Ltd., 240 Hedan Road, Shanghai 200131, China
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40
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Lenci E, Baldini L, Trabocchi A. Diversity-oriented synthesis as a tool to expand the chemical space of DNA-encoded libraries. Bioorg Med Chem 2021; 41:116218. [PMID: 34030087 DOI: 10.1016/j.bmc.2021.116218] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022]
Abstract
DNA-encoded libraries (DEL) represent a powerful technology for generating compound collections for drug discovery campaigns, that have allowed for the selection of many hit compounds over last three decades. However, the application of split-and-pool combinatorial methodologies, as well as the limitation imposed by DNA-compatible chemistry, has often brought to a limited exploration of the chemical space, with an over-representation of flat aromatic or peptide-like structures, whereas a higher scaffold complexity is generally associated with a more successful biological activity of the library. In this context, the application of Diversity-Oriented Synthesis, capable of creating sp3-rich molecular entities even starting from simple flat building blocks, can represent an efficient strategy to significantly broaden the chemical space explored by DELs. In this review, we present selected examples of DNA-compatible complexity-generating reactions that can be applied for the generation of DNA-encoded DOS libraries, including: (i) multicomponent reactions; (ii) C-H/C-X functionalization; (iii) tandem approaches; (iv) cycloadditions; (v) reactions introducing privileged elements. Also, selected case studies on the generation of DELs with high scaffold diversity are discussed, reporting their application in drug discovery programs.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Baldini
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019 Sesto Fiorentino, Italy; Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM), University of Florence, Viale Morgagni 85, 50134 Florence, Italy.
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41
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Large screening of DNA-compatible reaction conditions for Suzuki and Sonogashira cross-coupling reactions and for reverse amide bond formation. Bioorg Med Chem 2021; 41:116206. [PMID: 34038862 DOI: 10.1016/j.bmc.2021.116206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/02/2023]
Abstract
Progress in DNA-encoded chemical library synthesis and screening crucially relies on the availability of DNA-compatible reactions, which proceed with high yields and excellent purity for a large number of possible building blocks. In the past, experimental conditions have been presented for the execution of Suzuki and Sonogashira cross-coupling reactions on-DNA. In this article, our aim was to optimize Suzuki and Sonogashira reactions, comparing our results to previously published procedures. We have tested the performance of improved conditions using 606 building blocks (including boronic acids, pinacol boranes and terminal alkynes), achieving >70% conversion for 84% of the tested molecules. Moreover, we describe efficient experimental conditions for the on-DNA synthesis of amide bonds, starting from DNA derivatives carrying a carboxylic acid moiety and 300 primary, secondary and aromatic amines, as amide bonds are frequently found in DNA-encoded chemical libraries thanks to their excellent DNA compatibility.
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42
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Shi Y, Wu YR, Yu JQ, Zhang WN, Zhuang CL. DNA-encoded libraries (DELs): a review of on-DNA chemistries and their output. RSC Adv 2021; 11:2359-2376. [PMID: 35424149 PMCID: PMC8693808 DOI: 10.1039/d0ra09889b] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
A DNA-encoded library is a collection of small molecules covalently linked to DNA that has unique information about the identity and the structure of each library member. A DNA-encoded chemical library (DEL) is broadly adopted by major pharmaceutical companies and used in numerous drug discovery programs. The application of the DEL technology is advantageous at the initial period of drug discovery because of reduced cost, time, and storage space for the identification of target compounds. The key points for the construction of DELs comprise the development and the selection of the encoding methods, transfer of routine chemical reaction from off-DNA to on-DNA, and exploration of new chemical reactions on DNA. The limitations in the chemical space and the diversity of DEL were reduced gradually by using novel DNA-compatible reactions based on the formation and the cleavage of various bonds. Here, we summarized a series of novel DNA-compatible chemistry reactions for DEL building blocks and analysed the druggability of screened hit molecules via DELs in the past five years.
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Affiliation(s)
- Ying Shi
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Yan-Ran Wu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Jian-Qiang Yu
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
| | - Wan-Nian Zhang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
| | - Chun-Lin Zhuang
- School of Pharmacy, Key Laboratory of Hui Ethnic Medicine Modernization, Ministry of Education, Ningxia Medical University 1160 Shengli Street Yinchuan 750004 China
- School of Pharmacy, Second Military Medical University 325 Guohe Road Shanghai 200433 China
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43
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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44
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Huang Y, Meng L, Nie Q, Zhou Y, Chen L, Yang S, Fung YME, Li X, Huang C, Cao Y, Li Y, Li X. Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. Nat Chem 2020; 13:77-88. [PMID: 33349694 DOI: 10.1038/s41557-020-00605-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Membrane proteins on the cell surface perform a myriad of biological functions; however, ligand discovery for membrane proteins is highly challenging, because a natural cellular environment is often necessary to maintain protein structure and function. DNA-encoded chemical libraries (DELs) have emerged as a powerful technology for ligand discovery, but they are mainly limited to purified proteins. Here we report a method that can specifically label membrane proteins with a DNA tag, and thereby enable target-specific DEL selections against endogenous membrane proteins on live cells without overexpression or any other genetic manipulation. We demonstrate the generality and performance of this method by screening a 30.42-million-compound DEL against the folate receptor, carbonic anhydrase 12 and the epidermal growth factor receptor on live cells, and identify and validate a series of novel ligands for these targets. Given the high therapeutic significance of membrane proteins and their intractability to traditional high-throughput screening approaches, this method has the potential to facilitate membrane-protein-based drug discovery by harnessing the power of DEL.
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Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Langdong Chen
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yi Man Eva Fung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaomeng Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Cen Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK, Hong Kong SAR, China.
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45
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Yuen J, Chai J, Ding Y. Condensation of DNA-Conjugated Imines with Homophthalic Anhydride for the Synthesis of Isoquinolones on DNA. Bioconjug Chem 2020; 31:2712-2718. [DOI: 10.1021/acs.bioconjchem.0c00508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Josephine Yuen
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jing Chai
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Yun Ding
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
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46
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Kunig VBK, Potowski M, Akbarzadeh M, Klika Škopić M, dos Santos Smith D, Arendt L, Dormuth I, Adihou H, Andlovic B, Karatas H, Shaabani S, Zarganes‐Tzitzikas T, Neochoritis CG, Zhang R, Groves M, Guéret SM, Ottmann C, Rahnenführer J, Fried R, Dömling A, Brunschweiger A. TEAD-YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics. Angew Chem Int Ed Engl 2020; 59:20338-20342. [PMID: 32537835 PMCID: PMC7689693 DOI: 10.1002/anie.202006280] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/20/2020] [Indexed: 01/12/2023]
Abstract
DNA-encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or "hot spot", regions of protein-protein interactions. A DNA-encoded combinatorial peptoid library was designed based on the Ugi four-component reaction by employing tryptophan-mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide "hexT", encoded by DNA sequences, and substituted by azide-alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor-relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD-YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.
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Affiliation(s)
- Verena B. K. Kunig
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Marco Potowski
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Mohammad Akbarzadeh
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Mateja Klika Škopić
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Denise dos Santos Smith
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
| | - Lukas Arendt
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Ina Dormuth
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Hélène Adihou
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM)BioPharmaceuticals R&DAstraZeneca43150GothenburgSweden
- AstraZeneca-Max Planck Institute Satellite UnitMax-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Blaž Andlovic
- Lead Discovery Center GmbH (Germany)Otto-Hahn-Strasse 1544227DortmundGermany
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering and Institute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Hacer Karatas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Shabnam Shaabani
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | | | - Constantinos G. Neochoritis
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
- University of CreteDepartment of Chemistry70013HeraklionGreece
| | - Ran Zhang
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Matthew Groves
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Stéphanie M. Guéret
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM)BioPharmaceuticals R&DAstraZeneca43150GothenburgSweden
- AstraZeneca-Max Planck Institute Satellite UnitMax-Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Christian Ottmann
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering and Institute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Jörg Rahnenführer
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Roland Fried
- TU Dortmund UniversityFaculty of StatisticsVogelpothsweg 8744227DortmundGermany
| | - Alexander Dömling
- University of GroningenDrug DesignDeusinglaan 17313AVGroningenThe Netherlands
| | - Andreas Brunschweiger
- TU Dortmund UniversityFaculty of Chemistry and Chemical BiologyOtto-Hahn-Strasse 644227DortmundGermany
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47
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Tripolitsiotis NP, Thomaidi M, Neochoritis CG. The Ugi Three‐Component Reaction; a Valuable Tool in Modern Organic Synthesis. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001157] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Maria Thomaidi
- Chemistry Department School of Science and Engineering University of Crete 70013 Heraklion Greece
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48
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Bassi G, Favalli N, Vuk M, Catalano M, Martinelli A, Trenner A, Porro A, Yang S, Tham CL, Moroglu M, Yue WW, Conway SJ, Vogt PK, Sartori AA, Scheuermann J, Neri D. A Single-Stranded DNA-Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001970. [PMID: 33240760 PMCID: PMC7675038 DOI: 10.1002/advs.202001970] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 06/11/2023]
Abstract
A versatile and Lipinski-compliant DNA-encoded library (DEL), comprising 366 600 glutamic acid derivatives coupled to oligonucleotides serving as amplifiable identification barcodes is designed, constructed, and characterized. The GB-DEL library, constructed in single-stranded DNA format, allows de novo identification of specific binders against several pharmaceutically relevant proteins. Moreover, hybridization of the single-stranded DEL with a set of known protein ligands of low to medium affinity coupled to a complementary DNA strand results in self-assembled selectable chemical structures, leading to the identification of affinity-matured compounds.
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Affiliation(s)
- Gabriele Bassi
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Miriam Vuk
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Adriano Martinelli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Anika Trenner
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Antonio Porro
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Su Yang
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | - Chuin Lean Tham
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Wyatt W. Yue
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Peter K. Vogt
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
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49
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Busby SA, Carbonneau S, Concannon J, Dumelin CE, Lee Y, Numao S, Renaud N, Smith TM, Auld DS. Advancements in Assay Technologies and Strategies to Enable Drug Discovery. ACS Chem Biol 2020; 15:2636-2648. [PMID: 32880443 DOI: 10.1021/acschembio.0c00495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Assays drive drug discovery from the exploratory phases to the clinical testing of drug candidates. As such, numerous assay technologies and methodologies have arisen to support drug discovery efforts. Robust identification and characterization of tractable chemical matter requires biochemical, biophysical, and cellular approaches and often benefits from high-throughput methods. To increase throughput, efforts have been made to provide assays in miniaturized volumes which can be arrayed in microtiter plates to support the testing of as many as 100,000 samples/day. Alongside these efforts has been the growth of microtiter plate-free formats with encoded libraries that can support the screening of billions of compounds, a hunt for new drug modalities, as well as emphasis on more disease relevant formats using complex cell models of disease states. This review will focus on recent developments in high-throughput assay technologies applied to identify starting points for drug discovery. We also provide recommendations on strategies for implementing various assay types to select high quality leads for drug development.
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Affiliation(s)
- Scott A. Busby
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - John Concannon
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | | | - YounKyoung Lee
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Shin Numao
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Thomas M. Smith
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Douglas S. Auld
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
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Abstract
DNA-encoded library (DEL) technology is a novel ligand identification strategy that allows the synthesis and screening of unprecedented chemical diversity more efficiently than conventional methods. However, no reports have been published to systematically study how to increase the diversity and improve the molecular property space that can be covered with DEL. This report describes the development and application of eDESIGNER, an algorithm that comprehensively generates all possible library designs, enumerates and profiles samples from each library and evaluates them to select the libraries to be synthesized. This tool utilizes suitable on-DNA chemistries and available building blocks to design and identify libraries with a pre-defined molecular weight distribution and maximal diversity compared with compound collections from other sources.
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