1
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Yan KN, Nie YQ, Wang JY, Yin GL, Liu Q, Hu H, Sun X, Chen XH. Accelerating PROTACs Discovery Through a Direct-to-Biology Platform Enabled by Modular Photoclick Chemistry. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400594. [PMID: 38689503 PMCID: PMC11234393 DOI: 10.1002/advs.202400594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) have emerged as a promising strategy for drug discovery and exploring protein functions, offering a revolutionary therapeutic modality. Currently, the predominant approach to PROTACs discovery mainly relies on an empirical design-synthesis-evaluation process involving numerous cycles of labor-intensive synthesis-purification and bioassay data collection. Therefore, the development of innovative methods to expedite PROTAC synthesis and exploration of chemical space remains highly desired. Here, a direct-to-biology strategy is reported to streamline the synthesis of PROTAC libraries on plates, enabling the seamless transfer of reaction products to cell-based bioassays without the need for additional purification. By integrating amide coupling and light-induced primary amines and o-nitrobenzyl alcohols cyclization (PANAC) photoclick chemistry into a plate-based synthetic process, this strategy produces PROTAC libraries with high efficiency and structural diversity. Moreover, by employing this platform for PROTACs screening, we smoothly found potent PROTACs effectively inhibit triple-negative breast cancer (TNBC) cell growth and induce rapid, selective targeted degradation of cyclin-dependent kinase 9 (CDK9). The study introduces a versatile platform for assembling PROTACs on plates, followed by direct biological evaluation. This approach provides a promising opportunity for high-throughput synthesis of PROTAC libraries, thereby enhancing the efficiency of exploring chemical space and accelerating the discovery of PROTACs.
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Affiliation(s)
- Ke-Nian Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Qiang Nie
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Jia-Yu Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Guang-Liang Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qia Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiaoxia Sun
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang, 330013, China
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
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2
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Zhang J, Wang L, Ji Q, Liu F. DNA-Compatible Cyanomethylation of (Hetero)aryl Halides or Triflates under a Tandem Reaction for DNA-Encoded Library Synthesis. Org Lett 2023; 25:6931-6936. [PMID: 37677078 DOI: 10.1021/acs.orglett.3c02850] [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: 09/09/2023]
Abstract
A DNA-compatible reaction has been developed for the cyanomethylation of (hetero)aryl halides or triflates via a tandem process involving palladium-mediated Suzuki-Miyaura coupling and base-promoted isoxazole fragmentation. This one-pot protocol employs easily accessible starting materials, exhibits a wide substrate scope, and results in no significant DNA damage. Additionally, the resulting (hetero)arylacetonitriles can be converted into the corresponding carboxylic acids, which may be utilized for the synthesis of DNA-encoded chemical libraries.
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Affiliation(s)
- Jie Zhang
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing 211122, Jiangsu Province, China
| | - Lu Wang
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing 211122, Jiangsu Province, China
| | - Qian Ji
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing 211122, Jiangsu Province, China
| | - Fei Liu
- R&D Institute, Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing 211122, Jiangsu Province, China
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3
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Ertl P, Altmann E, Racine S, Decoret O. Which boronic acids are used most frequently for synthesis of bioactive molecules? Bioorg Med Chem 2023; 91:117405. [PMID: 37421711 DOI: 10.1016/j.bmc.2023.117405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
Boronic acids are essential building blocks used for the synthesis of bioactive molecules, the generation of chemical libraries and the exploration of structure-activity relationships. As a result, more than ten thousand boronic acids are commercially available. Medicinal chemists are therefore facing a challenge; which of them should they select to maximize information obtained by the synthesis of new target molecules. The present article aims to help them to make the right choices. The boronic acids used frequently in the synthesis of bioactive molecules were identified by mining several large molecular and reaction databases and their properties were analyzed. Based on the results a diverse set of boronic acids covering well the bioactive chemical space was selected and is suggested as a basis for library design for the efficient exploration of structure-activity relationships. A Boronic Acid Navigator web tool which helps chemists to make their own selection is also made available at https://bit.ly/boronics.
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Affiliation(s)
- Peter Ertl
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Eva Altmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sophie Racine
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Odile Decoret
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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4
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Chen JJ, Zhang JY, Fang JH, Du XY, Xia HD, Cheng B, Li N, Yu ZL, Bian JQ, Wang FL, Zheng JJ, Liu WL, Gu QS, Li ZL, Liu XY. Copper-Catalyzed Enantioconvergent Radical C(sp 3)-N Cross-Coupling of Activated Racemic Alkyl Halides with (Hetero)aromatic Amines under Ambient Conditions. J Am Chem Soc 2023. [PMID: 37392183 DOI: 10.1021/jacs.3c02387] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
The enantioconvergent C(sp3)-N cross-coupling of racemic alkyl halides with (hetero)aromatic amines represents an ideal means to afford enantioenriched N-alkyl (hetero)aromatic amines yet has remained unexplored due to the catalyst poisoning specifically for strong-coordinating heteroaromatic amines. Here, we demonstrate a copper-catalyzed enantioconvergent radical C(sp3)-N cross-coupling of activated racemic alkyl halides with (hetero)aromatic amines under ambient conditions. The key to success is the judicious selection of appropriate multidentate anionic ligands through readily fine-tuning both electronic and steric properties for the formation of a stable and rigid chelating Cu complex. Thus, this kind of ligand could not only enhance the reducing capability of a copper catalyst to provide an enantioconvergent radical pathway but also avoid the coordination with other coordinating heteroatoms, thereby overcoming catalyst poisoning and/or chiral ligand displacement. This protocol covers a wide range of coupling partners (89 examples for activated racemic secondary/tertiary alkyl bromides/chlorides and (hetero)aromatic amines) with high functional group compatibility. When allied with follow-up transformations, it provides a highly flexible platform to access synthetically useful enantioenriched amine building blocks.
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Affiliation(s)
- Ji-Jun Chen
- Shenzhen Key Laboratory of Cross-Coupling Reactions, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jia-Yong Zhang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Marine Biomedicine/Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Jia-Heng Fang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan-Yi Du
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hai-Dong Xia
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bin Cheng
- Institute of Marine Biomedicine/Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Nan Li
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhang-Long Yu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Qian Bian
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fu-Li Wang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jing-Jing Zheng
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei-Long Liu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qiang-Shuai Gu
- Academy for Advanced Interdisciplinary Studies and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhong-Liang Li
- Shenzhen Key Laboratory of Cross-Coupling Reactions, Southern University of Science and Technology, Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin-Yuan Liu
- Shenzhen Key Laboratory of Cross-Coupling Reactions, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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5
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Liu W, Mulhearn J, Hao B, Cañellas S, Last S, Gómez JE, Jones A, De Vera A, Kumar K, Rodríguez R, Van Eynde L, Strambeanu II, Wolkenberg SE. Enabling Deoxygenative C(sp 2)-C(sp 3) Cross-Coupling for Parallel Medicinal Chemistry. ACS Med Chem Lett 2023; 14:853-859. [PMID: 37312855 PMCID: PMC10258906 DOI: 10.1021/acsmedchemlett.3c00118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Herein we report the development of an automated deoxygenative C(sp2)-C(sp3) coupling of aryl bromide with alcohols to enable parallel medicinal chemistry. Alcohols are among the most diverse and abundant building blocks, but their usage as alkyl precursors has been limited. Although metallaphotoredox deoxygenative coupling is becoming a promising strategy to form C(sp2)-C(sp3) bond, the reaction setup limits its widespread application in library synthesis. To achieve high throughput and consistency, an automated workflow involving solid-dosing and liquid-handling robots has been developed. We have successfully demonstrated this high-throughput protocol is robust and consistent across three automation platforms. Furthermore, guided by cheminformatic analysis, we examined alcohols with comprehensive chemical space coverage and established a meaningful scope for medicinal chemistry applications. By accessing the rich diversity of alcohols, this automated protocol has the potential to substantially increase the impact of C(sp2)-C(sp3) cross-coupling in drug discovery.
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Affiliation(s)
- Wei Liu
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - James Mulhearn
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Bo Hao
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Santiago Cañellas
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Stefaan Last
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - José Enrique Gómez
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Alexander Jones
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - Alexander De Vera
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Kiran Kumar
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Raquel Rodríguez
- Discovery
Chemistry, Janssen Research & Development LLC, Janssen-Cilag, S.A., E-45007 Toledo, Spain
| | - Lars Van Eynde
- Discovery
Chemistry, Janssen Research & Development
LLC, 2340 Beerse, Belgium
| | - Iulia I. Strambeanu
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Scott E. Wolkenberg
- Discovery
Chemistry, Janssen Research & Development
LLC, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
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6
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Li X, Wang X, Zhang J. Ruthenium-catalysed decarboxylative unsymmetric dual ortho-/ meta-C-H bond functionalization of arenecarboxylic acids. Chem Sci 2023; 14:5470-5476. [PMID: 37234909 PMCID: PMC10208063 DOI: 10.1039/d3sc01226c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/04/2023] [Indexed: 05/28/2023] Open
Abstract
Here, we describe a ruthenium-catalysed decarboxylative unsymmetric ortho-C-H azaarylation/meta-C-H alkylation via a traceless directing group relay strategy. The installation of a 2-pyridyl functionality via carboxyl directed ortho-C-H activation is critical to promote decarboxylation and enable meta-C-H bond alkylation to streamline the synthesis of 4-azaaryl-benzo-fused five-membered heterocycles. This protocol is characterized by high regio- and chemoselectivity, broad substrate scopes, and good functional group tolerance under redox-neutral conditions.
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Affiliation(s)
- Xiankai Li
- The Institute for Advanced Studies, Wuhan University Wuhan Hubei Province 430072 China
| | - Xiaofei Wang
- The Institute for Advanced Studies, Wuhan University Wuhan Hubei Province 430072 China
| | - Jing Zhang
- The Institute for Advanced Studies, Wuhan University Wuhan Hubei Province 430072 China
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7
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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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8
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Cui Q, Song P, Ma T, Wang Z, Lu X, Shi Y, Zhang F, Lin G, Dong J, Zhang J. Discovery of a Novel Potent Antitumor Molecule, P19G1, by Erlotinib Derivative Libraries Synthesized by Modular Click-Chemistry. Technol Cancer Res Treat 2022; 21:15330338221109649. [PMID: 36303409 PMCID: PMC9619925 DOI: 10.1177/15330338221109649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Objective:Traditional chemical synthesis methods are cumbersome and inefficient. In this study, a novel antitumor molecule, 4-(4-(3-((6,7-bis(2-methoxyethoxy)quinazolin-4-yl)amino)phenyl)-1H-1,2,3-triazol-1-yl)phenyl sulfurofluoridate (P19G1), was identified by screening a library of Erlotinib derivatives synthesized by modular click chemistry, and the antitumor activity and underlying mechanism of P19G1 were further revealed. Methods: A series of Erlotinib derivatives (840 compounds) were synthesized using a modular click-chemistry method, and then the thiazolyl blue (MTT) method was used to screen and evaluate the inhibitory effect of these compounds on the growth and metastasis of A549 lung adenocarcinoma cells. Among them, the compound P19G1 showed the best inhibitory activity. Furthermore, the antitumor activity and mechanism of P19G1 were investigated with in vitro cell biology and in vivo assays in an animal model. Results: In vitro pharmacological studies showed that P19G1 had inhibitory effects on a variety of tumor cell lines with IC50 values in the range of 1 to 5 μM. Moreover, P19G1 significantly inhibited the proliferation and migration of the human lung adenocarcinoma cell line A549 and human colorectal cancer cell line RKO and promoted cell apoptosis. In vivo tumor-bearing mouse model experiments revealed that 50 mg/kg P19G1 effectively inhibited the growth and metastasis of A549 tumors without obvious toxicity to the host. Conclusions: The rapid structural modification of lead compounds using novel modular click-chemistry reactions holds great potential for use in obtaining diverse derivatives for tumor drug screening and development. P19G1 was discovered because of the application of click chemistry in this study, and it is an antitumor candidate molecule worthy of development.
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Affiliation(s)
- Qianfei Cui
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China
| | - Peng Song
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China,Key
Laboratory of Prevention and Treatment for Chronic Diseases By TCM,
Affiliated Hospital of Gansu University of Chinese
Medicine, Lanzhou, Gansu, China
| | - Tiancheng Ma
- Chinese Academy of Sciences, Shanghai Institute of Organic
Chemistry, Shanghai, China
| | - Zefeng Wang
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China
| | - Xiaojing Lu
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China
| | - Yongjia Shi
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China
| | - Fang Zhang
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China
| | - Guoqiang Lin
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China,Chinese Academy of Sciences, Shanghai Institute of Organic
Chemistry, Shanghai, China
| | - Jiajia Dong
- Chinese Academy of Sciences, Shanghai Institute of Organic
Chemistry, Shanghai, China,Jiajia Dong, Chinese Academy of Sciences,
Shanghai Institute of Organic Chemistry, Shanghai 200032, China.
| | - Jiange Zhang
- The Research Center of Chiral Drugs & Shanghai Frontiers Science
Center for Traditional Chinese Medicine Chemical Biology, Innovation Research
Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese
Medicine, Shanghai, China,Jiange Zhang, The Research Center of Chiral
Drugs & Shanghai Frontiers Science Center for Traditional Chinese Medicine
Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine
(IRI), Shanghai University of Traditional Chinese Medicine, Shanghai 201203,
China.
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9
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Xiong F, Yu M, Xu H, Zhong Z, Li Z, Guo Y, Zhang T, Zeng Z, Jin F, He X. Discovery of TIGIT inhibitors based on DEL and machine learning. Front Chem 2022; 10:982539. [PMID: 35958238 PMCID: PMC9360614 DOI: 10.3389/fchem.2022.982539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Drug discovery has entered a new period of vigorous development with advanced technologies such as DNA-encoded library (DEL) and artificial intelligence (AI). The previous DEL-AI combination has been successfully applied in the drug discovery of classical kinase and receptor targets mainly based on the known scaffold. So far, there is no report of the DEL-AI combination on inhibitors targeting protein-protein interaction, including those undruggable targets with few or unknown active scaffolds. Here, we applied DEL technology on the T cell immunoglobulin and ITIM domain (TIGIT) target, resulting in the unique hit compound 1 (IC50 = 20.7 μM). Based on the screening data from DEL and hit derivatives a1-a34, a machine learning (ML) modeling process was established to address the challenge of poor sample distribution uniformity, which is also frequently encountered in DEL screening on new targets. In the end, the established ML model achieved a satisfactory hit rate of about 75% for derivatives in a high-scored area.
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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,
| | - Mingao Yu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Honggui Xu
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | - Zhenmin Zhong
- 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
| | - Yuhan Guo
- Shenzhen NewDEL Biotech Co., Ltd., Shenzhen, China
| | | | - Zhixuan Zeng
- 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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10
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Melsen PRA, Yoshisada R, Jongkees SAK. Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries. Chembiochem 2022; 23:e202100685. [PMID: 35100479 PMCID: PMC9306583 DOI: 10.1002/cbic.202100685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Indexed: 11/07/2022]
Abstract
DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.
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Affiliation(s)
- Paddy R. A. Melsen
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Ryoji Yoshisada
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Seino A. K. Jongkees
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamDe Boelelaan 11081081 HZAmsterdamThe Netherlands
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11
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Cai K, Ran Y, Sun W, Gao S, Li J, Wan J, Liu G. Palladium-Mediated Hydroamination of DNA-Conjugated Aryl Alkenes. Front Chem 2022; 10:851674. [PMID: 35480389 PMCID: PMC9035600 DOI: 10.3389/fchem.2022.851674] [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: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
C-N bond formation is one of the most commonly used reactions in medicinal chemistry. Herein, we report an efficient Pd-promoted hydroamination reaction between DNA-conjugated aryl alkenes and a wide scope of aliphatic amines. The described reactions are demonstrated in good to excellent conversions to furnish C (sp3)–N bonds on DNA. This DNA-compatible transformation has strong potentials for the application into DNA-encoded library synthesis.
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Affiliation(s)
| | | | - Wenbo Sun
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
| | - Sen Gao
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
| | | | | | - Guansai Liu
- *Correspondence: Guansai Liu, ; Wenbo Sun, ; Sen Gao,
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12
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[4 + 1] Annulation of in situ generated azoalkenes with amines: A powerful approach to access 1-substituted 1,2,3-triazoles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Smedley CJ, Homer JA, Gialelis TL, Barrow AS, Koelln RA, Moses JE. Accelerated SuFEx Click Chemistry For Modular Synthesis. Angew Chem Int Ed Engl 2022; 61:e202112375. [PMID: 34755436 PMCID: PMC8867595 DOI: 10.1002/anie.202112375] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/20/2021] [Indexed: 01/23/2023]
Abstract
SuFEx click chemistry is a powerful method designed for the selective, rapid, and modular synthesis of functional molecules. Classical SuFEx reactions form stable S-O linkages upon exchange of S-F bonds with aryl silyl-ether substrates, and while near-perfect in their outcome, are sometimes disadvantaged by relatively high catalyst loadings and prolonged reaction times. We herein report the development of accelerated SuFEx click chemistry (ASCC), an improved SuFEx method for the efficient and catalytic coupling of aryl and alkyl alcohols with a range of SuFExable hubs. We demonstrate Barton's hindered guanidine base (2-tert-butyl-1,1,3,3-tetramethylguanidine; BTMG) as a superb SuFEx catalyst that, when used in synergy with silicon additive hexamethyldisilazane (HMDS), yields stable S-O bond linkages in a single step; often within minutes. The powerful combination of BTMG and HMDS reagents allows for catalyst loadings as low as 1.0 mol % and, in congruence with click-principles, provides a scalable method that is safe, efficient, and practical for modular synthesis. ASSC expands the number of accessible SuFEx products and will find significant application in organic synthesis, medicinal chemistry, chemical biology, and materials science.
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Affiliation(s)
| | - Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | - Andrew S. Barrow
- L. I. M. S., Science Dr, Bundoora, Melbourne, VIC 3086, Australia
| | - Rebecca A. Koelln
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA,
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14
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Smedley CJ, Homer JA, Gialelis TL, Barrow AS, Koelln RA, Moses JE. Accelerated SuFEx Click Chemistry For Modular Synthesis**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Joshua A. Homer
- Cancer Center Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor NY 11724 USA
| | | | | | - Rebecca A. Koelln
- Cancer Center Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor NY 11724 USA
| | - John E. Moses
- Cancer Center Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor NY 11724 USA
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15
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Billings KJ, Grenier-Davies MC. Library Synthesis: Building Block Selection, Handling, and Tracking. Methods Mol Biol 2022; 2541:1-11. [PMID: 36083536 DOI: 10.1007/978-1-0716-2545-3_1] [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
Careful selection and manipulation of small molecule building blocks is crucial to the success of a DNA-encoded library. Building block selection impacts the quality of the hits arising out of a selection assay, while proper sample handling and tracking ensure follow-up synthetic work is done with the appropriate synthetic map in mind. In this chapter, possible strategies for building block selection are outlined, as well as best practices for handling and tracking samples to be used for validation and library synthesis.
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Affiliation(s)
| | - Melissa C Grenier-Davies
- Encoded Library Technologies/NCE Molecular Discovery, R & D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
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16
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Zabolotna Y, Volochnyuk DM, Ryabukhin SV, Horvath D, Gavrilenko KS, Marcou G, Moroz YS, Oksiuta O, Varnek A. A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. J Chem Inf Model 2021; 62:2171-2185. [PMID: 34928600 DOI: 10.1021/acs.jcim.1c00811] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The ability to efficiently synthesize desired compounds can be a limiting factor for chemical space exploration in drug discovery. This ability is conditioned not only by the existence of well-studied synthetic protocols but also by the availability of corresponding reagents, so-called building blocks (BBs). In this work, we present a detailed analysis of the chemical space of 400 000 purchasable BBs. The chemical space was defined by corresponding synthons─fragments contributed to the final molecules upon reaction. They allow an analysis of BB physicochemical properties and diversity, unbiased by the leaving and protective groups in actual reagents. The main classes of BBs were analyzed in terms of their availability, rule-of-two-defined quality, and diversity. Available BBs were eventually compared to a reference set of biologically relevant synthons derived from ChEMBL fragmentation, in order to illustrate how well they cover the actual medicinal chemistry needs. This was performed on a newly constructed universal generative topographic map of synthon chemical space that enables visualization of both libraries and analysis of their overlapped and library-specific regions.
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Affiliation(s)
- Yuliana Zabolotna
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Dmitriy M Volochnyuk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Sergey V Ryabukhin
- The Institute of High Technologies, Kyiv National Taras Shevchenko University, 64 Volodymyrska Street, Kyiv 01601, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Dragos Horvath
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Konstantin S Gavrilenko
- Research-And-Education ChemBioCenter, National Taras Shevchenko University of Kyiv, Chervonotkatska str., 61, 03022 Kiev, Ukraine.,Enamine Ltd., 78 Chervonotkatska str., 02660 Kiev, Ukraine
| | - Gilles Marcou
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France
| | - Yurii S Moroz
- Research-And-Education ChemBioCenter, National Taras Shevchenko University of Kyiv, Chervonotkatska str., 61, 03022 Kiev, Ukraine.,Chemspace, Chervonotkatska Street 78, 02094 Kyiv, Ukraine
| | - Oleksandr Oksiuta
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv 02660, Ukraine.,Chemspace, Chervonotkatska Street 78, 02094 Kyiv, Ukraine
| | - Alexandre Varnek
- University of Strasbourg, Laboratoire de Chemoinformatique, 4, rue B. Pascal, Strasbourg 67081, France.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
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17
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Seierstad M, Tichenor MS, DesJarlais RL, Na J, Bacani GM, Chung DM, Mercado-Marin EV, Steffens HC, Mirzadegan T. Novel Reagent Space: Identifying Unorderable but Readily Synthesizable Building Blocks. ACS Med Chem Lett 2021; 12:1853-1860. [PMID: 34795876 DOI: 10.1021/acsmedchemlett.1c00340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/01/2021] [Indexed: 01/14/2023] Open
Abstract
Drug discovery building blocks available commercially or within an internal inventory cover a diverse range of chemical space and yet describe only a tiny fraction of all chemically feasible reagents. Vendors will eagerly provide tools to search the former; there is no straightforward method of mining the latter. We describe a procedure and use case in assembling chemical structures not available for purchase but that could likely be synthesized in one robust chemical transformation starting from readily available building blocks. Accessing this vast virtual chemical space dramatically increases our curated collection of reagents available for medicinal chemistry exploration and novel hit generation, almost tripling the number of those with 10 or fewer atoms.
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Affiliation(s)
- Mark Seierstad
- Janssen Research and Development, San Diego, California 92121, United States
| | - Mark S. Tichenor
- Janssen Research and Development, San Diego, California 92121, United States
| | - Renee L. DesJarlais
- Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Jim Na
- Janssen Research and Development, San Diego, California 92121, United States
| | - Genesis M. Bacani
- Janssen Research and Development, San Diego, California 92121, United States
| | - De Michael Chung
- Janssen Research and Development, San Diego, California 92121, United States
| | | | - Helena C. Steffens
- Janssen Research and Development, San Diego, California 92121, United States
| | - Taraneh Mirzadegan
- Janssen Research and Development, San Diego, California 92121, United States
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18
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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19
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Zhang Y, Clark MA. Design concepts for DNA-encoded library synthesis. Bioorg Med Chem 2021; 41:116189. [PMID: 34034150 DOI: 10.1016/j.bmc.2021.116189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
An approach of building block (BB) inclusivity and atom efficient library schemes deliver the quality and diversity of DNA-encoded libraries best suited for small molecule drug discovery. In this Perspective, we offer key learnings in DEL design from a decade's worth of DEL-driven screening.
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Affiliation(s)
- Y Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA
| | - M A Clark
- X-Chem Inc., 100 Beaver Street, Waltham, MA 02453, USA.
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20
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Guo AD, Wei D, Nie HJ, Hu H, Peng C, Li ST, Yan KN, Zhou BS, Feng L, Fang C, Tan M, Huang R, Chen XH. Light-induced primary amines and o-nitrobenzyl alcohols cyclization as a versatile photoclick reaction for modular conjugation. Nat Commun 2020; 11:5472. [PMID: 33122644 PMCID: PMC7596520 DOI: 10.1038/s41467-020-19274-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/30/2020] [Indexed: 12/31/2022] Open
Abstract
The advent of click chemistry has had a profound impact on many fields and fueled a need for reliable reactions to expand the click chemistry toolkit. However, developing new systems to fulfill the click chemistry criteria remains highly desirable yet challenging. Here, we report the development of light-induced primary amines and o-nitrobenzyl alcohols cyclization (PANAC) as a photoclick reaction via primary amines as direct click handle, to rapid and modular functionalization of diverse small molecules and native biomolecules. With intrinsic advantages of temporal control, good biocompatibility, reliable chemoselectivity, excellent efficiency, readily accessible reactants, operational simplicity and mild conditions, the PANAC photoclick is robust for direct diversification of pharmaceuticals and biorelevant molecules, lysine-specific modifications of unprotected peptides and native proteins in vitro, temporal profiling of endogenous kinases and organelle-targeted labeling in living systems. This strategy provides a versatile platform for organic synthesis, bioconjugation, medicinal chemistry, chemical biology and materials science.
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Affiliation(s)
- An-Di Guo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Dan Wei
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Hui-Jun Nie
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chengyuan Peng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shao-Tong Li
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Ke-Nian Yan
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Bin-Shan Zhou
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lei Feng
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Chao Fang
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ruimin Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Hua Chen
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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21
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Umuhire Juru A, Cai Z, Jan A, Hargrove AE. Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry. Chem Commun (Camb) 2020; 56:3555-3558. [PMID: 32104839 DOI: 10.1039/d0cc00266f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study establishes the applicability of imine-based dynamic combinatorial chemistry to discover non-covalent ligands for RNA targets. We elucidate properties underlying the reactivity of arylamines and demonstrate target-guided amplification of tight binders in an amiloride-based dynamic library.
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Affiliation(s)
- Aline Umuhire Juru
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Zhengguo Cai
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Adina Jan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
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22
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Tereshchenko OD, Perebiynis MY, Knysh IV, Vasylets OV, Sorochenko AA, Slobodyanyuk EY, Rusanov EB, Borysov OV, Kolotilov SV, Ryabukhin SV, Volochnyuk DM. Electrochemical Scaled‐up Synthesis of Cyclic Enecarbamates as Starting Materials for Medicinal Chemistry Relevant Building Bocks. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | | | | | | | - Eugeniy Y. Slobodyanyuk
- Enamine Ltd 78 Chervonotkatska str. Kyiv Ukraine
- Institute of Organic ChemistryNational Academy of Sciences of Ukraine 5 Murmanska str. Kyiv Ukraine
| | - Eduard B. Rusanov
- Institute of Organic ChemistryNational Academy of Sciences of Ukraine 5 Murmanska str. Kyiv Ukraine
| | - Oleksandr V. Borysov
- Enamine Ltd 78 Chervonotkatska str. Kyiv Ukraine
- Institute of Organic ChemistryNational Academy of Sciences of Ukraine 5 Murmanska str. Kyiv Ukraine
| | - Sergey V. Kolotilov
- L. V. Pisarzhevskii Institute of Physical ChemistryNational Academy of Sciences of Ukraine 31 Nauki ave. Kyiv Ukraine
| | - Sergey V. Ryabukhin
- Enamine Ltd 78 Chervonotkatska str. Kyiv Ukraine
- Taras Shevchenko National University of Kyiv 60 Volodymyrska str. Kyiv Ukraine
| | - Dmitriy M. Volochnyuk
- Enamine Ltd 78 Chervonotkatska str. Kyiv Ukraine
- Institute of Organic ChemistryNational Academy of Sciences of Ukraine 5 Murmanska str. Kyiv Ukraine
- Taras Shevchenko National University of Kyiv 60 Volodymyrska str. Kyiv Ukraine
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23
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Götte K, Chines S, Brunschweiger A. Reaction development for DNA-encoded library technology: From evolution to revolution? Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151889] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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25
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Clark PR, Williams GD, Hayes JF, Tomkinson NCO. A Scalable Metal‐, Azide‐, and Halogen‐Free Method for the Preparation of Triazoles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter R. Clark
- Chemical DevelopmentGlaxoSmithKline Gunnels Wood Road Stevenage SG1 2NY UK
- Department of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Glynn D. Williams
- Chemical DevelopmentGlaxoSmithKline Gunnels Wood Road Stevenage SG1 2NY UK
| | - Jerome F. Hayes
- Chemical DevelopmentGlaxoSmithKline Gunnels Wood Road Stevenage SG1 2NY UK
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied ChemistryUniversity of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
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26
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Clark PR, Williams GD, Hayes JF, Tomkinson NCO. A Scalable Metal-, Azide-, and Halogen-Free Method for the Preparation of Triazoles. Angew Chem Int Ed Engl 2020; 59:6740-6744. [PMID: 31943599 DOI: 10.1002/anie.201915944] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/06/2020] [Indexed: 11/08/2022]
Abstract
A scalable metal-, azide-, and halogen-free method for the synthesis of substituted 1,2,3-triazoles has been developed. The reaction proceeds through a 3-component coupling of α-ketoacetals, tosyl hydrazide, and a primary amine. The reaction shows outstanding functional-group tolerance with respect to both the α-ketoacetal and amine coupling partners, providing access to 4-, 1,4-, 1,5-, and 1,4,5-substituted triazoles in excellent yield. This robust method results in densely functionalised 1,2,3-triazoles that remain challenging to prepare by azide-alkyne cycloaddition (AAC, CuAAC, RuAAC) methods and can be scaled in either batch or flow reactors. Methods for the chemoselective reaction of either aliphatic amines or anilines are also described, revealing some of the potential of this novel and highly versatile transformation.
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Affiliation(s)
- Peter R Clark
- Chemical Development, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK.,Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Glynn D Williams
- Chemical Development, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Jerome F Hayes
- Chemical Development, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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27
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Kapadiya KM, Dhalani JM, Patel BY. Green Regioselective Synthesis of (Purin-6-yl)hydrazones. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428019100178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Grygorenko OO, Volochnyuk DM, Ryabukhin SV, Judd DB. The Symbiotic Relationship Between Drug Discovery and Organic Chemistry. Chemistry 2019; 26:1196-1237. [PMID: 31429510 DOI: 10.1002/chem.201903232] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Indexed: 12/20/2022]
Abstract
All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.
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Affiliation(s)
- Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kiev, 02660, Ukraine
| | - Sergey V Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Duncan B Judd
- Awridian Ltd., Stevenage Bioscience Catalyst, Gunnelswood Road, Stevenage, Herts, SG1 2FX, UK
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29
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Feng G, Wang X, Jin J. Decarboxylative C-C and C-N Bond Formation by Ligand-Accelerated Iron Photocatalysis. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901381] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Guangshou Feng
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
| | - Xiaofei Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
- College of Chemistry and Materials Science; Shanghai Normal University; 100 Guilin Road 200234 Shanghai China
| | - Jian Jin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances; Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry; University of Chinese Academy of Sciences, Chinese Academy of Sciences; 345 Lingling Road 200032 Shanghai China
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30
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Modular click chemistry libraries for functional screens using a diazotizing reagent. Nature 2019; 574:86-89. [PMID: 31578481 DOI: 10.1038/s41586-019-1589-1] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/08/2019] [Indexed: 12/20/2022]
Abstract
Click chemistry is a concept in which modular synthesis is used to rapidly find new molecules with desirable properties1. Copper(I)-catalysed azide-alkyne cycloaddition (CuAAC) triazole annulation and sulfur(VI) fluoride exchange (SuFEx) catalysis are widely regarded as click reactions2-4, providing rapid access to their products in yields approaching 100% while being largely orthogonal to other reactions. However, in the case of CuAAC reactions, the availability of azide reagents is limited owing to their potential toxicity and the risk of explosion involved in their preparation. Here we report another reaction to add to the click reaction family: the formation of azides from primary amines, one of the most abundant functional groups5. The reaction uses just one equivalent of a simple diazotizing species, fluorosulfuryl azide6-11 (FSO2N3), and enables the preparation of over 1,200 azides on 96-well plates in a safe and practical manner. This reliable transformation is a powerful tool for the CuAAC triazole annulation, the most widely used click reaction at present. This method greatly expands the number of accessible azides and 1,2,3-triazoles and, given the ubiquity of the CuAAC reaction, it should find application in organic synthesis, medicinal chemistry, chemical biology and materials science.
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31
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Li JY, Miklossy G, Modukuri RK, Bohren KM, Yu Z, Palaniappan M, Faver JC, Riehle K, Matzuk MM, Simmons N. Palladium-Catalyzed Hydroxycarbonylation of (Hetero)aryl Halides for DNA-Encoded Chemical Library Synthesis. Bioconjug Chem 2019; 30:2209-2215. [PMID: 31329429 PMCID: PMC6706801 DOI: 10.1021/acs.bioconjchem.9b00447] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A strategy
for DNA-compatible, palladium-catalyzed hydroxycarbonylation
of (hetero)aryl halides on DNA–chemical conjugates has been
developed. This method generally provided the corresponding carboxylic
acids in moderate to very good conversions for (hetero)aryl iodides
and bromides, and in poor to moderate conversions for (hetero)aryl
chlorides. These conditions were further validated by application
within a DNA-encoded chemical library synthesis and subsequent discovery
of enriched features from the library in selection experiments against
two protein targets.
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Affiliation(s)
- Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Gabriella Miklossy
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Ram K Modukuri
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - John C Faver
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Kevin Riehle
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Nicholas Simmons
- Center for Drug Discovery, Department of Pathology and Immunology , Baylor College of Medicine , Houston , Texas 77030 , United States
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32
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Li Z, Wang X, Xia S, Jin J. Ligand-Accelerated Iron Photocatalysis Enabling Decarboxylative Alkylation of Heteroarenes. Org Lett 2019; 21:4259-4265. [PMID: 31090423 DOI: 10.1021/acs.orglett.9b01439] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A mild, practical protocol for the decarboxylative alkylation of heteroarenes has been accomplished via iron photocatalysis. A diverse range of carboxylic acids readily undergo oxidative decarboxylation and then couple with a broad array of heteroarenes in this transformation. The photoexcited state lifetimes of iron complexes are typically much shorter than those of iridium and ruthenium complexes. Here we describe our effort on iron photocatalysis by utilizing the intramolecular charge transfer pathway of iron-carboxylate complexes.
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Affiliation(s)
- Zhenlong Li
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Xiaofei Wang
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Siqi Xia
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Jian Jin
- CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
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33
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Berger O, Winters KR, Sabourin A, Dzyuba SV, Montchamp JL. On the cost of academic methodologies. Org Chem Front 2019. [DOI: 10.1039/c9qo00200f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Synthetic methodologies can be easily compared using the Cost of Academic Methodologies (CAM) parameter, which estimates the cost of making a mole of a product.
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Affiliation(s)
- Olivier Berger
- Department of Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
| | - Karen R. Winters
- Department of Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
| | - Axel Sabourin
- Department of Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
| | - Sergei V. Dzyuba
- Department of Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
| | - Jean-Luc Montchamp
- Department of Chemistry and Biochemistry
- Texas Christian University
- Fort Worth
- USA
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34
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Valeur E, Jimonet P. New Modalities, Technologies, and Partnerships in Probe and Lead Generation: Enabling a Mode-of-Action Centric Paradigm. J Med Chem 2018; 61:9004-9029. [DOI: 10.1021/acs.jmedchem.8b00378] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eric Valeur
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 431 83, Sweden
| | - Patrick Jimonet
- External Innovation Drug Discovery, Global Business Development & Licensing, Sanofi, 13 quai Jules Guesde, 94400 Vitry-sur-Seine, France
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35
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Gualandi A, Savoini A, Saporetti R, Franchi P, Lucarini M, Cozzi PG. A facile hydroxylation of arylboronic acids mediated by sodium ascorbate. Org Chem Front 2018. [DOI: 10.1039/c8qo00061a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A mild and selective method for the synthesis of phenols has been described.
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Affiliation(s)
- Andrea Gualandi
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
| | - Andrea Savoini
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
| | - Roberto Saporetti
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
| | - Paola Franchi
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
| | - Marco Lucarini
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “G. Ciamician”
- ALMA MATER STUDIORUM Università di Bologna
- 40126 Bologna
- Italy
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36
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Huang H, Yu C, Li X, Zhang Y, Zhang Y, Chen X, Mariano PS, Xie H, Wang W. Synthesis of Aldehydes by Organocatalytic Formylation Reactions of Boronic Acids with Glyoxylic Acid. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- He Huang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Chenguang Yu
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Xiangmin Li
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Yongqiang Zhang
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Yueteng Zhang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Xiaobei Chen
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Patrick S. Mariano
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Hexin Xie
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Wei Wang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
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37
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Huang H, Yu C, Li X, Zhang Y, Zhang Y, Chen X, Mariano PS, Xie H, Wang W. Synthesis of Aldehydes by Organocatalytic Formylation Reactions of Boronic Acids with Glyoxylic Acid. Angew Chem Int Ed Engl 2017; 56:8201-8205. [DOI: 10.1002/anie.201703127] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- He Huang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Chenguang Yu
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Xiangmin Li
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Yongqiang Zhang
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Yueteng Zhang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Xiaobei Chen
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Patrick S. Mariano
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
| | - Hexin Xie
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
| | - Wei Wang
- Department of Chemistry & Chemical Biology University of New Mexico Albuquerque NM 87131 USA
- State Key Laboratory of Bioengineering Reactor and Shanghai Key Laboratory of New Drug Design, School of Pharmacy East China University of Science & Technology 130 Mei-Long Road Shanghai 200237 P.R. China
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38
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Highly Stereoselective Synthesis of a Compound Collection Based on the Bicyclic Scaffolds of Natural Products. Molecules 2017; 22:molecules22050827. [PMID: 28524077 PMCID: PMC6153746 DOI: 10.3390/molecules22050827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/17/2022] Open
Abstract
Despite the great contribution of natural products in the history of successful drug discovery, there are significant limitations that persuade the pharmaceutical industry to evade natural products in drug discovery research. The extreme scarcity as well as structural complexity of natural products renders their practical synthetic access and further modifications extremely challenging. Although other alternative technologies, particularly combinatorial chemistry, were embraced by the pharmaceutical industry to get quick access to a large number of small molecules with simple frameworks that often lack three-dimensional complexity, hardly any success was achieved in the discovery of lead molecules. To acquire chemotypes beholding structural features of natural products, for instance high sp³ character, the synthesis of compound collections based on core-scaffolds of natural products presents a promising strategy. Here, we report a natural product inspired synthesis of six different chemotypes and their derivatives for drug discovery research. These bicyclic hetero- and carbocyclic scaffolds are highly novel, rich in sp³ features and with ideal physicochemical properties to display drug likeness. The functional groups on the scaffolds were exploited further to generate corresponding compound collections. Synthesis of two of these collections exemplified with ca. 350 compounds are each also presented. The whole compound library is being exposed to various biological screenings within the European Lead Factory consortium.
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39
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Karawajczyk A, Orrling KM, de Vlieger JSB, Rijnders T, Tzalis D. The European Lead Factory: A Blueprint for Public-Private Partnerships in Early Drug Discovery. Front Med (Lausanne) 2017; 3:75. [PMID: 28154815 PMCID: PMC5243859 DOI: 10.3389/fmed.2016.00075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 12/23/2016] [Indexed: 11/17/2022] Open
Abstract
The European Lead Factory (ELF) is a public–private partnership (PPP) that provides researchers in Europe with a unique platform for translation of innovative biology and chemistry into high-quality starting points for drug discovery. It combines an exceptional collection of small molecules, high-throughput screening (HTS) infrastructure, and hit follow-up capabilities to advance research projects from both private companies and publicly funded researchers. By active interactions with the wider European life science community, ELF connects and unites bright ideas, talent, and experience from several disciplines. As a result, ELF is a unique, collaborative lead generation engine that has so far resulted in >4,500 hit compounds with a defined biological activity from 83 successfully completed HTS and hit evaluation campaigns. The PPP has also produced more than 120,000 novel innovative library compounds that complement the 327,000 compounds contributed by the participating pharmaceutical companies. Intrinsic to its setup, ELF enables breakthroughs in areas with unmet medical and societal needs, where no individual entity would be able to create a comparable impact in such a short time.
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40
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Goodnow RA, Davie CP. DNA-Encoded Library Technology: A Brief Guide to Its Evolution and Impact on Drug Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
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42
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Li Y, Gabriele E, Samain F, Favalli N, Sladojevich F, Scheuermann J, Neri D. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries. ACS COMBINATORIAL SCIENCE 2016; 18:438-43. [PMID: 27314981 DOI: 10.1021/acscombsci.6b00058] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
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Affiliation(s)
- Yizhou Li
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Elena Gabriele
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Nicholas Favalli
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | | | - Jörg Scheuermann
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
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43
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Stotani S, Lorenz C, Winkler M, Medda F, Picazo E, Ortega Martinez R, Karawajczyk A, Sanchez-Quesada J, Giordanetto F. Design and Synthesis of Fsp(3)-Rich, Bis-Spirocyclic-Based Compound Libraries for Biological Screening. ACS COMBINATORIAL SCIENCE 2016; 18:330-6. [PMID: 27163646 DOI: 10.1021/acscombsci.6b00005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The exploration of innovative chemical space is a critical step in the early phases of drug discovery. Bis-spirocyclic frameworks occur in natural products and other biologically relevant metabolites and show attractive features, such as molecular compactness, structural complexity, and three-dimensional character. A concise approach to the synthesis of bis-spirocyclic-based compound libraries starting from readily available commercial reagents and robust chemical transformations has been developed. A number of novel bis-spirocyclic scaffold examples, as implemented in the European Lead Factory project, is presented.
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Affiliation(s)
- Silvia Stotani
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Christoph Lorenz
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Matthias Winkler
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Federico Medda
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Edwige Picazo
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Raquel Ortega Martinez
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Anna Karawajczyk
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Jorge Sanchez-Quesada
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
| | - Fabrizio Giordanetto
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, 44227 Dortmund, Germany
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44
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Affiliation(s)
- Raphael M. Franzini
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Cassie Randolph
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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45
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Flagstad T, Min G, Bonnet K, Morgentin R, Roche D, Clausen MH, Nielsen TE. Synthesis of sp3-rich scaffolds for molecular libraries through complexity-generating cascade reactions. Org Biomol Chem 2016; 14:4943-6. [DOI: 10.1039/c6ob00961a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An efficient strategy for the synthesis of complex small molecules from simple building blocks is presented.
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Affiliation(s)
- T. Flagstad
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
- Center for Nanomedicine and Theranostics
| | - G. Min
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
- Center for Nanomedicine and Theranostics
| | | | | | | | - M. H. Clausen
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
- Center for Nanomedicine and Theranostics
| | - T. E. Nielsen
- Department of Chemistry
- Technical University of Denmark
- DK-2800 Kgs. Lyngby
- Denmark
- Singapore Centre on Environmental Life Sciences Engineering
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46
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Škopić MK, Bugain O, Jung K, Onstein S, Brandherm S, Kalliokoski T, Brunschweiger A. Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00243a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-encoded libraries based on scaffolds functionalized for DNA-compatible chemistry were synthesized by split-and-pool combinatorial chemistry. The library design was aided by a chemoinformatic filtering cascade.
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Affiliation(s)
- M. Klika Škopić
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - O. Bugain
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - K. Jung
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Onstein
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Brandherm
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | | | - A. Brunschweiger
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
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