1
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Dong J, Yu D, Li T, Xue D. Recent advances in the synthesis of bicyclo[4.1.1]octanes. Org Biomol Chem 2025. [PMID: 40364773 DOI: 10.1039/d5ob00533g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
The exploration of bicyclo[n.1.1]alkanes, known for their intricate chemical diversity and potential as benzene bioisosteres, has garnered significant attention over the past two decades. In particular, the past year has seen the emergence of bicyclo[4.1.1]octanes and their structural analogues as promising bioisosteres for meta-substituted arenes and cis-1,3-disubstituted cyclohexanes. To meet the growing demand for bicyclo[4.1.1]octanes, chemists have recently developed innovative (4 + 3) cycloaddition strategies, leveraging bicyclobutanes (BCBs) and 1,4-dipoles for their synthesis. This review provides a comprehensive evaluation of recent advancements in the synthesis and functionalization of these compounds, emphasizing their scope and underlying mechanisms. Additionally, we highlight the challenges and future prospects of identifying novel reaction pathways to access new functionalized bicyclo[4.1.1]octanes.
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Affiliation(s)
- Jianyang Dong
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, China.
| | - Dejiang Yu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, China.
| | - Ting Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, China.
| | - Dong Xue
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710062, China.
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2
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Tyler JL, Trauner D, Glorius F. Reaction development: a student's checklist. Chem Soc Rev 2025; 54:3272-3292. [PMID: 39912730 DOI: 10.1039/d4cs01046a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2025]
Abstract
So you've discovered a reaction. But how do you turn this new discovery into a fully-fledged program that maximises the potential of your novel transformation? Herein, we provide a student's checklist to serve as a helpful guide for synthesis development, allowing you to thoroughly investigate the chemistry in question while ensuring that no key aspect of the project is overlooked. A wide variety of the most illuminating synthetic and spectroscopic techniques will be summarised, in conjunction with literature examples and our own insights, to provide sound justifications for their implementation towards the goal of developing new reactions.
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Affiliation(s)
- Jasper L Tyler
- University of Muenster, Institute for Organic Chemistry, Corrensstrasse 36, 48149 Muenster, Germany.
| | - Dirk Trauner
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.
| | - Frank Glorius
- University of Muenster, Institute for Organic Chemistry, Corrensstrasse 36, 48149 Muenster, Germany.
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3
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Pitchai M, K C N, Ulaganathan S, Javeed M, Ramirez A, Srinivas P, Roy S, Traeger SC, Mignone J, Jurica EA, Pabbisetty KB, Vetrichelvan M, Gupta A, Mathur A, Mandler MD. Shapeshifting Gabriel Amine Synthesis with Iodo-BCPs. J Org Chem 2025; 90:3468-3474. [PMID: 39984299 DOI: 10.1021/acs.joc.5c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2025]
Abstract
The Gabriel amine synthesis is a textbook method for the preparation of primary amines from alkyl halides. In this work, we demonstrate a Gabriel amine synthesis with iodo-bicyclopentanes to make aminomethyl bicyclobutanes. DFT studies support the concerted rearrangement of a bicyclo[1.1.1]pentyl to a bicyclo[1.1.0]butyl carbocation, initiated by a carbon-halide dissociation. A carboxamide substituent stabilizes the carbocation intermediate with anchimeric assistance.
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Affiliation(s)
- Manivel Pitchai
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Nanjundaswamy K C
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Sankar Ulaganathan
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Mohammad Javeed
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Antonio Ramirez
- Bristol Myers Squibb Chemical Process Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Pavan Srinivas
- Analytical Research & Development, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Sourav Roy
- Analytical Research & Development, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Sarah C Traeger
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - James Mignone
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Elizabeth A Jurica
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Kumar B Pabbisetty
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Muthalagu Vetrichelvan
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Anuradha Gupta
- Department of Discovery Synthesis, Biocon Bristol Myers Squibb R&D Centre, Biocon Park, Plot No. 2 & 3, Jigani Link Road, Bommasandra IV, Bangalore 560100, India
| | - Arvind Mathur
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Michael D Mandler
- Bristol Myers Squibb Research, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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4
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Sercel ZP, Marek I. Access to Quaternary-Substituted Cyclobutylsilanes by Ring Opening of Arylbicyclobutanes with Silyllithium Reagents. Angew Chem Int Ed Engl 2025; 64:e202421235. [PMID: 39887918 DOI: 10.1002/anie.202421235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 01/21/2025] [Accepted: 01/29/2025] [Indexed: 02/01/2025]
Abstract
Disclosed herein is the reaction of silyllithium reagents with quaternary-substituted arylbicyclobutanes to diastereoselectively form polysubstituted cyclobutylsilanes by C-C bond cleavage. The bicyclobutanes are generated in situ, by lithium-halogen exchange, from readily accessible (bromomethyl)iodocyclopropane precursors, rendering this a one-pot transformation. The trapping of a generated cyclobutyllithium intermediate with an electrophile was also demonstrated, providing a cyclobutane product with vicinal quaternary stereocenters. The utility of the cyclobutylsilane products was showcased by Tamao-Fleming oxidation to prepare a quaternary-substituted cyclobutanol.
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Affiliation(s)
- Zachary P Sercel
- Schulich Faculty of Chemistry and the Resnick Sustainability Center for catalysis. Technion -, Israel Institute of Technology Technion City, Haifa, 3200009, Israel
| | - Ilan Marek
- Schulich Faculty of Chemistry and the Resnick Sustainability Center for catalysis. Technion -, Israel Institute of Technology Technion City, Haifa, 3200009, Israel
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5
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Lyu B, Gou W, Xu F, Chen L, Wang Z, Ren Z, Liu G, Li Y, Hou W. Target Discovery Driven by Chemical Biology and Computational Biology. CHEM REC 2025; 25:e202400182. [PMID: 39811950 DOI: 10.1002/tcr.202400182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 12/06/2024] [Indexed: 01/16/2025]
Abstract
Target identification is crucial for drug screening and development because it can reveal the mechanism of drug action and ensure the reliability and accuracy of the results. Chemical biology, an interdisciplinary field combining chemistry and biology, can assist in this process by studying the interactions between active molecular compounds and proteins and their physiological effects. It can also help predict potential drug targets or candidates, develop new biomarker assays and diagnostic reagents, and evaluate the selectivity and range of active compounds to reduce the risk of off-target effects. Chemical biology can achieve these goals using techniques such as changing protein thermal stability, enzyme sensitivity, and molecular structure and applying probes, isotope labeling and mass spectrometry. Concurrently, computational biology employs a diverse array of computational models to predict drug targets. This approach also offers innovative avenues for repurposing existing drugs. In this paper, we review the reported chemical biology and computational biology techniques for identifying different types of targets that can provide valuable insights for drug target discovery.
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Affiliation(s)
- Bohai Lyu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Wenfeng Gou
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Feifei Xu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Leyuan Chen
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhiyun Wang
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Zhonghao Ren
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Department of Pharmacology, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, China
| | - Gaiting Liu
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yiliang Li
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Wenbin Hou
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
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6
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Chu JC, Tsai KC, Wang TY, Chen TY, Tsai JY, Lee T, Lin MH, Hsieh YSY, Wu CC, Huang WJ. Discovery and biological evaluation of potent 2-trifluoromethyl acrylamide warhead-containing inhibitors of protein disulfide isomerase. Eur J Med Chem 2025; 283:117169. [PMID: 39708767 DOI: 10.1016/j.ejmech.2024.117169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 12/08/2024] [Accepted: 12/11/2024] [Indexed: 12/23/2024]
Abstract
Protein disulfide isomerase (PDI) regulates multiple protein functions by catalyzing the oxidation, reduction, and isomerization of disulfide bonds. The enzyme is considered a potential target for treating thrombosis. We previously developed a potent PDI inhibitor, CPD, which contains the propiolamide as a warhead targeting cysteine residue in PDI. To address its issues with undesirable off-target effects and weak metabolic stability, we replaced the propiolamide group with various electrophiles. Among these, compound 2d, which contains 2-trifluoromethyl acrylamide exhibited potent PDI inhibition compared to the reference PACMA31. Further structural optimization of compound 2d led to a novel series of 2-trifluoromethyl acrylamide derivatives. Several of these compounds displayed substantially improved enzyme inhibition. Notably, compound 14d demonstrated the strongest inhibition against PDI, with an IC50 value of 0.48 ± 0.004 μM. Additionally, compound 14d was found to exhibit a reversible binding mode with PDI enzyme. Further biological evaluations show that 14d suppressed platelet aggregation and thrombus formation by attenuating GPIIb/IIIa activation without significantly causing cytotoxicity. Altogether, these findings suggest PDI inhibitors could be a potential strategy for anti-thrombosis.
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Affiliation(s)
- Jung-Chun Chu
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan; Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ting-Yu Wang
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tzu-Yin Chen
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Ju-Ying Tsai
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tien Lee
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mei-Hsiang Lin
- School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yves S Y Hsieh
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, SE-10691, Sweden
| | - Chin-Chung Wu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Wei-Jan Huang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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7
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Zhong Z, Hocking BJW, Brown CP, Ma TK, White AJP, Mann DJ, Armstrong A, Bull JA. Synthesis and Functionalization of Sulfoximine-Bicyclo[1.1.0]butanes: Functionalizable, Tuneable and Cysteine-Selective Chiral Warheads. Angew Chem Int Ed Engl 2025; 64:e202420028. [PMID: 39551713 DOI: 10.1002/anie.202420028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/15/2024] [Accepted: 11/16/2024] [Indexed: 11/19/2024]
Abstract
Electrophilic covalent warheads with appropriate reactivity and selectivity are crucial to the investigation of protein function and the discovery of therapeutics. Here we report the synthesis of sulfoximine bicyclo[1.1.0] butanes (BCBs) as novel thiol reactive chiral warheads, achieved in one-pot from methylsulfoximines. Unusually the warhead can then be derivatized, keeping the BCB intact, over 3 vectors: i) sulfoximine N-modification instills a broad range of strain-release reactivity; ii) sp2-cross-coupling reactions on aryl-BCB-sulfoximines allows direct diversification, and iii) functionalization of the BCB motif itself is achieved by metalation and trapping with electrophiles. The BCB sulfoximines are shown to react selectively with cysteine including in a protein model (CDK2) under biocompatible conditions. Preliminary data indicate suitability for chemoproteomic applications, and enantioselective cysteine-labelling. The reactivity of sulfoximine BCBs with electron withdrawing groups on nitrogen is comparable to acrylamides with low to moderate reactivity.
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Affiliation(s)
- Zhenhao Zhong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Brad J W Hocking
- Department of Life Sciences, Imperial College London South Kensington Campus, London, SW7 2AZ, UK
| | - Charles P Brown
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Tsz-Kan Ma
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Andrew J P White
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - David J Mann
- Department of Life Sciences, Imperial College London South Kensington Campus, London, SW7 2AZ, UK
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - James A Bull
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
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8
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Chang M, Xu H, Dong Y, Gnawali G, Bi F, Wang W. Dual-Performing Vinyltetrazine for Rapid, Selective Bioconjugation and Functionalization of Cysteine Proteins. ACS Chem Biol 2025; 20:153-161. [PMID: 39707969 PMCID: PMC11747768 DOI: 10.1021/acschembio.4c00610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2024]
Abstract
Although methods for Cys-specific bioconjugation and functionalization of proteins have been developed and widely utilized in biomolecule engineering and therapeutic development, reagents for this purpose are generally designed to accomplish bioconjugation only. Consequently, additional clickable groups must be attached to these reagents to accomplish functionalization. Herein, we describe a new, simple, dual-performing bioconjugation-functionalization reagent, VMeTz, which possesses an electron-withdrawing tetrazine (Tz) substituted vinyl (V) moiety to serve as both a Michael receptor for selective conjugation with Cys and a site for click with TCO derivatives to introduce functionality. Critically, VMeTz contains a methyl group that prevents the formation of multiple Tz-containing Cys-adducts. Reactions of VMeTz with Cys-containing peptides and proteins both in vitro and in live cells produce single stable Michael adducts with high selectivity. Moreover, the Cys-VMeTz peptide and protein conjugates undergo facile click reactions with TCO-functionalized reagents for labeling and protein profiling. Furthermore, VMeTz selectively activates and delivers the TCO-caged toxic substances Dox and PROTAC ARV-771 to cancer cells to produce therapeutic effects that are comparable to those of the parent drugs. Collectively, the studies demonstrate that VMeTz is a useful reagent for therapeutically significant Cys-specific protein bioconjugation and functionalization.
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Affiliation(s)
- Mengyang Chang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Hang Xu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Yue Dong
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Giri Gnawali
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Fangchao Bi
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, and BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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9
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Liang J, Tian J, Zhang H, Li H, Chen L. Proteomics: An In-Depth Review on Recent Technical Advances and Their Applications in Biomedicine. Med Res Rev 2025. [PMID: 39789883 DOI: 10.1002/med.22098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 10/11/2024] [Accepted: 12/12/2024] [Indexed: 01/12/2025]
Abstract
Proteins hold pivotal importance since many diseases manifest changes in protein activity. Proteomics techniques provide a comprehensive exploration of protein structure, abundance, and function in biological samples, enabling the holistic characterization of overall changes in organisms. Nowadays, the breadth of emerging methodologies in proteomics is unprecedentedly vast, with constant optimization of technologies in sample processing, data collection, data analysis, and its scope of application is steadily transitioning from the bench to the clinic. Here, we offer an insightful review of the technical developments in proteomics and its applications in biomedicine over the past 5 years. We focus on its profound contributions in profiling disease spectra, discovering new biomarkers, identifying promising drug targets, deciphering alterations in protein conformation, and unearthing protein-protein interactions. Moreover, we summarize the cutting-edge technologies and potential breakthroughs in the proteomics pipeline and provide the principal challenges in proteomics. Based on these, we aspire to broaden the applicability of proteomics and inspire researchers to enhance our understanding of complex biological systems by utilizing such techniques.
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Affiliation(s)
- Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jundan Tian
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Huadong Zhang
- College of Pharmacy, Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
- College of Pharmacy, Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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10
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Wang W, Xiao JA, Zheng L, Liang WJ, Yang L, Huang XX, Lin C, Chen K, Su W, Yang H. Structure-Dependent, Switchable Alder-Ene/[2π + 2σ] Cycloadditions of Vinyl Bicyclo[1.1.0]butanes with α-Ketoesters Enabled by Palladium Catalysis. Org Lett 2024; 26:10645-10650. [PMID: 39628401 DOI: 10.1021/acs.orglett.4c04251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2024]
Abstract
A structure-dependent, palladium-catalyzed switchable alder-ene/[2π + 2σ] cycloaddition of VBCBs with α-ketoesters has been reported. A variety of cyclobutenes and 2-oxabicyclo[2.1.1]hexanes have been efficiently achieved in good to excellent yields through strain-release-driven alder-ene reactions and [2π + 2σ] cycloadditions, respectively. The potential of this method is illustrated by the scale-up reaction and diverse postsynthetic transformations of the obtained cyclic scaffolds. Additionally, the reaction mechanism and origins of the chemoselectivity have been probed by computational studies.
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Affiliation(s)
- Wei Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Jun-An Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Lan Zheng
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Wen-Jie Liang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Liu Yang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Xiao-Xiang Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Chenxiang Lin
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Kai Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, People's Republic of China
| | - Wei Su
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, People's Republic of China
| | - Hua Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, People's Republic of China
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11
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Deswal S, Guin A, Biju AT. Lewis Acid-Catalyzed Unusual (4+3) Annulation of para-Quinone Methides with Bicyclobutanes: Access to Oxabicyclo[4.1.1]Octanes. Angew Chem Int Ed Engl 2024; 63:e202408610. [PMID: 39171678 DOI: 10.1002/anie.202408610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 08/23/2024]
Abstract
Over the past few years, there has been a surge of interest in the chemistry of bicyclobutanes (BCBs). Although BCBs have been used to synthesize bicyclo[2.1.1]hexanes and bicyclo[3.1.1]heptanes, the synthesis of bicyclo[4.1.1]octanes has remained elusive. Herein, we report the first Lewis acid-catalyzed unexpected (4+3) annulation of para-quinonemethides (p-QMs) with BCBs allowing the synthesis of oxabicyclo[4.1.1]octanes proceeding under mild conditions. With 5 mol % of Bi(OTf)3, the reaction afforded the (4+3) annulated product in high regioselectivity and good functional group compatibility via a simultaneous Lewis acid activation of BCBs and p-QMs. The reaction is likely initiated by the 1,6-addition of Lewis acid activated BCBs to p-QMs followed by the C2-selective intramolecular addition of the phenol moiety to the generated cyclobutyl cation intermediate. Moreover, detailed mechanistic studies provided insight into the mechanism of the reaction.
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Affiliation(s)
- Shiksha Deswal
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Avishek Guin
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Akkattu T Biju
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
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12
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Liu J, Qian Y, Zhao H, Liu Y, Qin Z, Zhang Z, Rong L. Electrochemical Selenized Reaction of N-Arylbicyclo[1.1.0]butane-1-carboxamides: Access to 3-(Arylselanyl)spiro[cyclobutane-1,3'-indolin]-2'-one Derivatives. J Org Chem 2024; 89:15914-15923. [PMID: 39440833 DOI: 10.1021/acs.joc.4c02085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
A novel selenized reaction of N-arylbicyclo [1.1.0]butane-1-carboxamides with diselenide for the synthesis of polycyclic indoline derivatives is developed under electrochemical conditions. The synthesis is achieved by the bicyclo[1.1.0]butane strain-release reaction and intramolecular cyclization process. In addition, this approach features a wide range of substrates, good group tolerance, shorter reaction time, and mild conditions.
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Affiliation(s)
- Jiyao Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Yuliang Qian
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Haicheng Zhao
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Yun Liu
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Zhenglong Qin
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Zifeng Zhang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
| | - Liangce Rong
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
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13
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Guin A, Deswal S, Harariya MS, Biju AT. Lewis acid-catalyzed diastereoselective formal ene reaction of thioindolinones/thiolactams with bicyclobutanes. Chem Sci 2024; 15:12473-12479. [PMID: 39118603 PMCID: PMC11304820 DOI: 10.1039/d4sc02194k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/25/2024] [Indexed: 08/10/2024] Open
Abstract
Bicyclo[1.1.0]butanes (BCBs), featuring two fused cyclopropane rings, have found widespread application in organic synthesis. Their versatile reactivity towards radicals, nucleophiles, cations, and carbenes makes them suitable for various reactions, including ring-opening and annulation strategies. Despite this versatility, their potential as enophiles in an ene reaction remains underexplored. Considering this and given the challenges of achieving diastereoselectivity in ring-opening reactions of BCBs, herein, we present a unique method utilizing BCBs as enophiles in a mild and diastereoselective Sc(OTf)3-catalyzed formal ene reaction with thioindolinones/thiolactams, delivering 1,3-disubstituted cyclobutane derivatives in high yields and excellent regio- and diastereoselectivity. Notably, structurally different thiolactam derivatives underwent diastereoselective addition to BCBs, affording the corresponding cyclobutanes. The synthesized thioindole-substituted cyclobutanes could serve as a versatile tool for subsequent functional group manipulations.
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Affiliation(s)
- Avishek Guin
- Department of Organic Chemistry, Indian Institute of Science Bangalore 560012 India https://atbiju.in/
| | - Shiksha Deswal
- Department of Organic Chemistry, Indian Institute of Science Bangalore 560012 India https://atbiju.in/
| | - Mahesh Singh Harariya
- Department of Organic Chemistry, Indian Institute of Science Bangalore 560012 India https://atbiju.in/
| | - Akkattu T Biju
- Department of Organic Chemistry, Indian Institute of Science Bangalore 560012 India https://atbiju.in/
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14
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Xia PF, Zhou J, Yuan J, Zeng R, Liu Y, Tang KW, Fan JH. Oxidative Difunctionalization of N-Aryl Bicyclobutyl Amides with Aldehydes: Divergent Synthesis of Acylated and Alkylated 3-Spirocyclobutyl Oxindoles. Org Lett 2024; 26:6486-6490. [PMID: 39042855 DOI: 10.1021/acs.orglett.4c02325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
An efficient and operationally simple oxidative radical difunctionalization of N-aryl bicyclobutyl (BCB) amides with aldehydes is described. It was found that acylated 3-spirocyclobutyl oxindoles were generated from the coupling of BCB-amides and aromatic aldehydes, while reactions gave exclusively decarbonylative alkylarylation products using alkyl aldehydes as radical precursors.
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Affiliation(s)
- Peng-Fei Xia
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jiao Zhou
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jing Yuan
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Rui Zeng
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Yu Liu
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Ke-Wen Tang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jian-Hong Fan
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
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15
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Sterling AJ, Smith RC, Anderson EA, Duarte F. Beyond Strain Release: Delocalization-Enabled Organic Reactivity. J Org Chem 2024; 89:9979-9989. [PMID: 38970491 PMCID: PMC11267611 DOI: 10.1021/acs.joc.4c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/08/2024]
Abstract
The release of strain energy is a fundamental driving force for organic reactions. However, absolute strain energy alone is an insufficient predictor of reactivity, evidenced by the similar ring strain but disparate reactivity of cyclopropanes and cyclobutanes. In this work, we demonstrate that electronic delocalization is a key factor that operates alongside strain release to boost, or even dominate, reactivity. This delocalization principle extends across a wide range of molecules containing three-membered rings such as epoxides, aziridines, and propellanes and also applies to strain-driven cycloaddition reactions. Our findings lead to a "rule of thumb" for the accurate prediction of activation barriers in such systems, which can be easily applied to reactions involving many of the strained building blocks commonly encountered in organic synthesis, medicinal chemistry, polymer science, and bioconjugation. Given the significance of electronic delocalization in organic chemistry, for example in aromatic π-systems and hyperconjugation, we anticipate that this concept will serve as a versatile tool to understand and predict organic reactivity.
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Affiliation(s)
- Alistair J. Sterling
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Chemistry & Biochemistry, The University
of Texas at Dallas, 800
W. Campbell Rad, Richardson, Texas 75080, United States
| | - Russell C. Smith
- Abbvie
Drug Discovery Science & Technology (DDST), 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Edward A. Anderson
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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16
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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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17
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Walther R, Park M, Ashman N, Welch M, Carroll JS, Spring DR. Tuneable thiol exchange linkers for traceless drug release applications in prodrugs and ADCs. Chem Commun (Camb) 2024; 60:7025-7028. [PMID: 38888299 PMCID: PMC11223184 DOI: 10.1039/d4cc01558d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
We describe a versatile and tuneable thiol responsive linker system using thiovinylketones, which relies on the conjugate addition-elimination mechanism of Michael acceptors for the traceless release of therapeutics. In a proof-of-principle study, we translate our findings to exhibit potent thiol-cleavable antibiotic prodrugs and antibody-drug conjugates.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Mahri Park
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Nicola Ashman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, Robinson Way, CB2 0RE Cambridge, UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
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18
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Tyler J, Schäfer F, Shao H, Stein C, Wong A, Daniliuc CG, Houk KN, Glorius F. Bicyclo[1.1.0]butyl Radical Cations: Synthesis and Application to [2π + 2σ] Cycloaddition Reactions. J Am Chem Soc 2024; 146:16237-16247. [PMID: 38811005 PMCID: PMC11177261 DOI: 10.1021/jacs.4c04403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
As the chemistry that surrounds the field of strained hydrocarbons, such as bicyclo[1.1.0]butane, continues to expand, it becomes increasingly advantageous to develop alternative reactivity modes that harness their unique properties to access new regions of chemical space. Herein, we report the use of photoredox catalysis to promote the single-electron oxidation of bicyclo[1.1.0]butanes. The synthetic utility of the resulting radical cations is highlighted by their ability to undergo highly regio- and diastereoselective [2π + 2σ] cycloaddition reactions. The most notable feature of this transformation is the breadth of alkene classes that can be employed, including nonactivated alkenes, which have so far been elusive for previous strategies. A rigorous mechanistic investigation, in conjunction with DFT computation, was undertaken in order to better understand the physical nature of bicyclo[1.1.0]butyl radical cations and thus provides a platform from which further studies into the synthetic applications of these intermediates can be built upon.
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Affiliation(s)
- Jasper
L. Tyler
- Organisch-Chemisches
Institut, Universität Münster, 48149 Münster, Germany
| | - Felix Schäfer
- Organisch-Chemisches
Institut, Universität Münster, 48149 Münster, Germany
| | - Huiling Shao
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Colin Stein
- Organisch-Chemisches
Institut, Universität Münster, 48149 Münster, Germany
| | - Audrey Wong
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | | | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Frank Glorius
- Organisch-Chemisches
Institut, Universität Münster, 48149 Münster, Germany
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19
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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20
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Suresh R, Orbach N, Marek I. Synthesis of Stereodefined Polysubstituted Bicyclo[1.1.0]butanes. J Am Chem Soc 2024; 146:13748-13753. [PMID: 38722207 PMCID: PMC11117409 DOI: 10.1021/jacs.4c04438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
We report a highly diastereoselective synthesis of polysubstituted bicyclobutanes possessing up to three stereodefined quaternary centers and five substituents. Our strategy involves a diastereoselective carbometalation of cyclopropenes followed by a cyclization to furnish the bicyclobutane ring system. This straightforward approach allows for the incorporation of a diverse range of substituents and functional groups, notably without the need for electron-withdrawing functionalities.
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Affiliation(s)
- Rahul Suresh
- Schulich Faculty of Chemistry
and The Resnick Sustainability Center for Catalysis, Technion−Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Noam Orbach
- Schulich Faculty of Chemistry
and The Resnick Sustainability Center for Catalysis, Technion−Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | - Ilan Marek
- Schulich Faculty of Chemistry
and The Resnick Sustainability Center for Catalysis, Technion−Israel Institute of Technology, Technion City, Haifa 32000, Israel
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21
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Yan J, Dong L, Yang Y, Zhang D. DFT Insight into a Strain-Release Mechanism in Bicyclo[1.1.0]butanes via Concerted Activation of Central and Lateral C-C Bonds with Rh(III) Catalysis. Inorg Chem 2024; 63:8879-8888. [PMID: 38676642 DOI: 10.1021/acs.inorgchem.4c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Transition-metal-catalyzed, strain-release-driven transformations of "spring-loaded" bicyclo[1.1.0]butanes (BCBs) are considered potent tools in synthetic organic chemistry. Previously proposed strain-release mechanisms involve either the insertion of the central C-C bond of BCBs into a metal-carbon bond, followed by β-C elimination, or the oxidative addition of the central or lateral C-C bond on the transition metal center, followed by reductive elimination. This study, employing DFT calculations on a Rh(III)-catalyzed model system in a three-component protocol involving oxime ether, BCB ester, and ethyl glyoxylate for constructing diastereoselective quaternary carbon centers, introduces an unusual strain-release mechanism for BCBs. In this mechanism, the catalytic reaction is initiated by the simultaneous cleavage of two C-C bonds (the central and lateral C-C bonds), resulting in the formation of a Rh-carbene intermediate. The new mechanism exhibits a barrier of 21.0 kcal/mol, making it energetically more favorable by 11.1 kcal/mol compared to the previously suggested most favorable pathway. This unusual reaction mode rationalizes experimental observation of the construction of quaternary carbon centers, including the excellent E-selectivity and diastereoselectivity. The newly proposed strain-release mechanism holds promise in advancing our understanding of transition-metal-catalyzed C-C bond activation mechanisms and facilitating the synthesis of transition metal carbene complexes.
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Affiliation(s)
- Jing Yan
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, Shandong, China
| | - Lihua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, Shandong, China
| | - Yiying Yang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Dongju Zhang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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22
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Wang T, Ma S, Ji G, Wang G, Liu Y, Zhang L, Zhang Y, Lu H. A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell. Nat Commun 2024; 15:2997. [PMID: 38589397 PMCID: PMC11001985 DOI: 10.1038/s41467-024-47033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Cell surface proteins are responsible for many crucial physiological roles, and they are also the major category of drug targets as the majority of therapeutics target membrane proteins on the surface of cells to alter cellular signaling. Despite its great significance, ligand discovery against membrane proteins has posed a great challenge mainly due to the special property of their natural habitat. Here, we design a new chemical proteomic probe OPA-S-S-alkyne that can efficiently and selectively target the lysines exposed on the cell surface and develop a chemical proteomics strategy for global analysis of surface functionality (GASF) in living cells. In total, we quantified 2639 cell surface lysines in Hela cell and several hundred residues with high reactivity were discovered, which represents the largest dataset of surface functional lysine sites to date. We discovered and validated that hyper-reactive lysine residues K382 on tyrosine kinase-like orphan receptor 2 (ROR2) and K285 on Endoglin (ENG/CD105) are at the protein interaction interface in co-crystal structures of protein complexes, emphasizing the broad potential functional consequences of cell surface lysines and GASF strategy is highly desirable for discovering new active and ligandable sites that can be functionally interrogated for drug discovery.
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Affiliation(s)
- Ting Wang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Shiyun Ma
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guanghui Ji
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Yang Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China
| | - Ying Zhang
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
| | - Haojie Lu
- Liver Cancer Institute, Zhongshan Hospital and Department of Chemistry, Fudan University, Shanghai, China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Shanghai, China.
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23
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Fan JH, Yuan J, Xia PF, Zhou J, Zhong LJ, Huang PF, Liu Y, Tang KW, Li JH. Photoredox-Catalyzed Alkylarylation of N-Aryl Bicyclobutyl Amides with α-Carbonyl Alkyl Bromides: Access to 3-Spirocyclobutyl Oxindoles. Org Lett 2024; 26:2073-2078. [PMID: 38446422 DOI: 10.1021/acs.orglett.4c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
A visible-light-induced radical alkylarylation of N-aryl bicyclobutyl amides with α-carbonyl alkyl bromides for the synthesis of functionalized 3-spirocyclobutyl oxindoles is described in which β-selective radical addition of the alkyl radical to N-aryl bicyclobutyl amides forms a key radical intermediate followed by interception with intrinsic arene functional group. This approach can be applicable to a wide range of α-carbonyl alkyl bromides, including primary, secondary, and tertiary α-bromoalkyl esters, ketones, nitriles, and nitro compounds.
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Affiliation(s)
- Jian-Hong Fan
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jing Yuan
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Peng-Fei Xia
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jiao Zhou
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Long-Jin Zhong
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Peng-Fei Huang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Yu Liu
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Ke-Wen Tang
- Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Jin-Heng Li
- State Key Laboratory Base of Eco-Chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
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24
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Jiang Z, Tang Y, Lu J, Xu C, Niu Y, Zhang G, Yang Y, Cheng X, Tong L, Chen Z, Tang B. Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins. Redox Biol 2024; 69:102969. [PMID: 38064764 PMCID: PMC10755098 DOI: 10.1016/j.redox.2023.102969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 01/01/2024] Open
Abstract
Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.
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Affiliation(s)
- Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yue Tang
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, PR China.
| | - Jun Lu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Chang Xu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China; Laoshan Laboratory, Qingdao, 266200, PR China.
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25
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McNamee RE, Frank N, Christensen KE, Duarte F, Anderson EA. Taming nonclassical carbocations to control small ring reactivity. SCIENCE ADVANCES 2024; 10:eadj9695. [PMID: 38215201 PMCID: PMC10786418 DOI: 10.1126/sciadv.adj9695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Prediction of the outcome of ring opening of small organic rings under cationic conditions can be challenging due to the intermediacy of nonclassical carbocations. For example, the solvolysis of cyclobutyl or cyclopropylmethyl derivatives generates up to four products on nucleophilic capture or elimination via cyclopropylcarbinyl and bicyclobutonium ions. Here, we show that such reaction outcomes can be controlled by subtle changes to the structure of nonclassical carbocation. Using bicyclo[1.1.0]butanes as cation precursors, the regio- and stereochemistry of ring opening is shown to depend on the degree and nature of the substituents on the cationic intermediates. Reaction outcomes are rationalized using computational models, resulting in a flowchart to predict product formation from a given cation precursor.
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Affiliation(s)
| | | | | | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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26
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McNamee RE, Dasgupta A, Christensen KE, Anderson EA. Bridge Cross-Coupling of Bicyclo[1.1.0]butanes. Org Lett 2024; 26:360-364. [PMID: 38156902 PMCID: PMC10789093 DOI: 10.1021/acs.orglett.3c04030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Bicyclo[1.1.0]butanes (BCBs) have gained growing popularity in "strain release" chemistry for the synthesis of four-membered-ring systems and para- and meta-disubstituted arene bioisosteres as well as applications in chemoselective bioconjugation. However, functionalization of the bridge position of BCBs can be challenging due to the inherent strain of the ring system and reactivity of the central C-C bond. Here we report the first late-stage bridge cross-coupling of BCBs, mediated by directed metalation/palladium catalysis.
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Affiliation(s)
- Ryan E. McNamee
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ayan Dasgupta
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kirsten E. Christensen
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Edward A. Anderson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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27
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Dasgupta A, Bhattacharjee S, Tong Z, Guin A, McNamee RE, Christensen KE, Biju AT, Anderson EA. Stereoselective Alder-Ene Reactions of Bicyclo[1.1.0]butanes: Facile Synthesis of Cyclopropyl- and Aryl-Substituted Cyclobutenes. J Am Chem Soc 2024; 146:1196-1203. [PMID: 38157245 PMCID: PMC10786042 DOI: 10.1021/jacs.3c13080] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Bicyclo[1.1.0]butanes (BCBs), strained carbocycles comprising two fused cyclopropane rings, have become well-established building blocks in organic synthesis, medicinal chemistry, and chemical biology due to their diverse reactivity profile with radicals, nucleophiles, cations, and carbenes. The constraints of the bicyclic ring system confer high p-character on the interbridgehead C-C bond, leading to this broad reaction profile; however, the use of BCBs in pericyclic processes has to date been largely overlooked in favor of such stepwise, non-concerted additions. Here, we describe the use of BCBs as substrates for ene-like reactions with strained alkenes and alkynes, which give rise to cyclobutenes decorated with highly substituted cyclopropanes and arenes. The former products are obtained from highly stereoselective reactions with cyclopropenes, generated in situ from vinyl diazoacetates under blue light irradiation (440 nm). Cyclobutenes featuring a quaternary aryl-bearing carbon atom are prepared from equivalent reactions with arynes, which proceed in high yields under mild conditions. Mechanistic studies highlight the importance of electronic effects in this chemistry, while computational investigations support a concerted pathway and rationalize the excellent stereoselectivity of reactions with cyclopropenes.
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Affiliation(s)
- Ayan Dasgupta
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Subrata Bhattacharjee
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
| | - Zixuan Tong
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Avishek Guin
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
| | - Ryan E. McNamee
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kirsten E. Christensen
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Akkattu T. Biju
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
| | - Edward A. Anderson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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28
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Liu D, Guo X, Zhou S, Guo L, Zhang X. Mechanistic Insight into Lewis Acid-Catalyzed Cycloaddition of Bicyclo[1.1.0]butanes with Ketene: Bicyclo[1.1.0]butanes Serving as an Electrophile. J Org Chem 2024. [PMID: 38163764 DOI: 10.1021/acs.joc.3c02452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Lewis acid-catalyzed cycloaddition between bicyclo[1.1.0]butanes (BCBs) and unsaturated substrates has recently been demonstrated to be a powerful strategy for synthesizing bicyclo[2.1.1]hexanes. However, their reaction mechanisms remain elusive. This computational work explored the recently developed TMSOTf-catalyzed cycloaddition of BCB ketone to ketene and determined the rate-determining step as the activation of BCB ketone. Contrary to the previous proposal of BCB enolate as the active species, this work instead identified the catalytically active species to be a partially Lewis acid-activated BCB cation, which shows a greater electrophilicity and larger orbital interactions with ketene compared to those of the pristine BCB. The most favorable reaction pathway uniquely utilizes this activated BCB species as an electrophile to react with ketene as a nucleophile, while the previously proposed enolate is relatively inactive. Moreover, the in situ-generated TfO anion is revealed to be non-innocent, and its coordination mode and orientation could affect the reaction kinetics.
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Affiliation(s)
- Dan Liu
- School of Sciences, Great Bay University, Dongguan 523000, China
- Great Bay Institute for Advanced Study, Dongguan 523000, China
- Institute of Flexible Electronics (IFE), Northwestern Polytechnical University (NPU), 127 West Youyi Road, 710000 Shaanxi, China
| | - Xuefeng Guo
- Institute of Flexible Electronics (IFE), Northwestern Polytechnical University (NPU), 127 West Youyi Road, 710000 Shaanxi, China
| | - Shaoyuan Zhou
- School of Light Industry and Materials, Guangdong Polytechnic, Gaoming, Foshan 528000, China
| | - Luxuan Guo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Xiaoyong Zhang
- School of Sciences, Great Bay University, Dongguan 523000, China
- Great Bay Institute for Advanced Study, Dongguan 523000, China
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29
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Kawano M, Murakawa S, Higashiguchi K, Matsuda K, Tamura T, Hamachi I. Lysine-Reactive N-Acyl- N-aryl Sulfonamide Warheads: Improved Reaction Properties and Application in the Covalent Inhibition of an Ibrutinib-Resistant BTK Mutant. J Am Chem Soc 2023; 145:26202-26212. [PMID: 37987622 DOI: 10.1021/jacs.3c08740] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The covalent inhibition of a target protein has gained widespread attention in the field of drug discovery. Most of the current covalent drugs utilize the high reactivity of cysteines toward modest electrophiles. However, there is a growing need for warheads that can target lysine residues to expand the range of covalently druggable proteins and to deal with emerging proteins with mutations resistant to cysteine-targeted covalent drugs. We have recently developed an N-acyl-N-alkyl sulfonamide (NASA) as a lysine-targeted electrophile. Despite its successful application, this NASA warhead suffered from instability in physiological environments, such as serum-containing medium, because of its high intrinsic reactivity. In this study, we sought to modify the structure of the NASA warhead and found that N-acyl-N-aryl sulfonamides (ArNASAs) are promising electrophiles for use in a lysine-targeted covalent inhibition strategy. We prepared a focused library of ArNASA derivatives with diverse structures and reactivity and identified several warhead candidates with suppressed hydrolysis-mediated inactivation and reduced nonspecific reactions with off-target proteins, without sacrificing the reactivity toward the target. These reaction properties enabled the improved covalent inhibition of intracellular heat shock protein 90 (HSP90) in the presence of serum and the development of the first irreversible inhibitor for ibrutinib-resistant Bruton's tyrosine kinase (BTK) bearing the C481S mutation. This study clearly demonstrated the use of a set of ArNASA warheads to create highly potent covalent drugs and highlighted the importance of enriching the current arsenal of lysine-reactive warheads.
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Affiliation(s)
- Masaharu Kawano
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Syunsuke Murakawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Higashiguchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Matsuda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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30
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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31
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Ni D, Hu S, Tan X, Yu Y, Li Z, Deng L. Intermolecular Formal Cycloaddition of Indoles with Bicyclo[1.1.0]butanes by Lewis Acid Catalysis. Angew Chem Int Ed Engl 2023; 62:e202308606. [PMID: 37583090 DOI: 10.1002/anie.202308606] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
Herein, we develop a new approach to directly access architecturally complex polycyclic indolines from readily available indoles and bicyclo[1.1.0]butanes (BCBs) through formal cycloaddition promoted by commercially available Lewis acids. The reaction proceeded through a stepwise pathway involving a nucleophilic addition of indoles to BCBs followed by an intramolecular Mannich reaction to form rigid indoline-fused polycyclic structures, which resemble polycyclic indole alkaloids. This new reaction tolerated a wide range of indoles and BCBs, thereby allowing the one-step construction of various rigid indoline polycycles containing up to four contiguous quaternary carbon centers.
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Affiliation(s)
- Dongshun Ni
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
| | - Sai Hu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
| | - Xiangyu Tan
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
| | - Yang Yu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
| | - Zhenghua Li
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
| | - Li Deng
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, 310030, Zhejiang Province, China
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32
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Xiao Y, Xu TT, Zhou JL, Wu F, Tang L, Liu RY, Wu WB, Feng JJ. Photochemical α-selective radical ring-opening reactions of 1,3-disubstituted acyl bicyclobutanes with alkyl halides: modular access to functionalized cyclobutenes. Chem Sci 2023; 14:13060-13066. [PMID: 38023515 PMCID: PMC10664698 DOI: 10.1039/d3sc04457b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Although ring-opening reactions of bicyclobutanes bearing electron-withdrawing groups, typically with β-selectivity, have evolved as a powerful platform for synthesis of cyclobutanes, their application in the synthesis of cyclobutenes remains underdeveloped. Here, a novel visible light induced α-selective radical ring-opening reaction of 1,3-disubstituted acyl bicyclobutanes with alkyl radical precursors for the synthesis of functionalized cyclobutenes is described. In particular, primary, secondary, and tertiary alkyl halides are all suitable substrates for this photocatalytic transformation, providing ready access to cyclobutenes with a single all-carbon quaternary center, or with two contiguous centers under mild reaction conditions.
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Affiliation(s)
- Yuanjiu Xiao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Tong-Tong Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Jin-Lan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Feng Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Lei Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Ruo-Yi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Wen-Biao Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
| | - Jian-Jun Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Advanced Catalytic Engineering Research Center of the Ministry of Education, College of Chemistry and Chemical Engineering, Hunan University Changsha Hunan 410082 P. R. China
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33
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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34
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Mandler MD, Mignone J, Jurica EA, Palkowitz MD, Aulakh D, Cauley AN, Farley CA, Zhang S, Traeger SC, Sarjeant A, Paiva A, Perez HL, Ellsworth BA, Regueiro-Ren A. Synthesis of Bicyclo[1.1.0]butanes from Iodo-Bicyclo[1.1.1]pentanes. Org Lett 2023; 25:7947-7952. [PMID: 37284784 DOI: 10.1021/acs.orglett.3c01417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We describe a two-step process for the synthesis of substituted bicyclo[1.1.0]butanes. A photo-Hunsdiecker reaction generates iodo-bicyclo[1.1.1]pentanes under metal-free conditions at room temperature. These intermediates react with nitrogen and sulfur nucleophiles to afford substituted bicyclo[1.1.0]butane products.
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Affiliation(s)
- Michael D Mandler
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - James Mignone
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Elizabeth A Jurica
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Maximilian D Palkowitz
- Bristol Myers Squibb, Research & Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Darpandeep Aulakh
- Bristol Myers Squibb, Chemical & Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Anthony N Cauley
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Christopher A Farley
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Shasha Zhang
- Bristol Myers Squibb, Chemical & Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Sarah C Traeger
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Amy Sarjeant
- Bristol Myers Squibb, Chemical & Synthetic Development, 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Anthony Paiva
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Heidi L Perez
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Bruce A Ellsworth
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Alicia Regueiro-Ren
- Bristol Myers Squibb, Research & Early Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
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35
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Ding H, Lyu J, Zhang XL, Xiao X, Liu XW. Efficient and versatile formation of glycosidic bonds via catalytic strain-release glycosylation with glycosyl ortho-2,2-dimethoxycarbonylcyclopropylbenzoate donors. Nat Commun 2023; 14:4010. [PMID: 37419914 PMCID: PMC10329021 DOI: 10.1038/s41467-023-39619-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Catalytic glycosylation is a vital transformation in synthetic carbohydrate chemistry due to its ability to expediate the large-scale oligosaccharide synthesis for glycobiology studies with the consumption of minimal amounts of promoters. Herein we introduce a facile and efficient catalytic glycosylation employing glycosyl ortho-2,2-dimethoxycarbonylcyclopropylbenzoates (CCBz) promoted by a readily accessible and non-toxic Sc(III) catalyst system. The glycosylation reaction involves a novel activation mode of glycosyl esters driven by the ring-strain release of an intramolecularly incorporated donor-acceptor cyclopropane (DAC). The versatile glycosyl CCBz donor enables highly efficient construction of O-, S-, and N-glycosidic bonds under mild conditions, as exemplified by the convenient preparation of the synthetically challenging chitooligosaccharide derivatives. Of note, a gram-scale synthesis of tetrasaccharide corresponding to Lipid IV with modifiable handles is achieved using the catalytic strain-release glycosylation. These attractive features promise this donor to be the prototype for developing next generation of catalytic glycosylation.
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Affiliation(s)
- Han Ding
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Jian Lyu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Xiao-Lin Zhang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Xiong Xiao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University (NPU), Xi'an, 710072, P.R. China.
| | - Xue-Wei Liu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore.
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36
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Koo TY, Lai H, Nomura DK, Chung CYS. N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics. Nat Commun 2023; 14:3564. [PMID: 37322008 PMCID: PMC10272157 DOI: 10.1038/s41467-023-39268-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cysteine has been exploited as the binding site of covalent drugs. Its high sensitivity to oxidation is also important for regulating cellular processes. To identify new ligandable cysteines which can be hotspots for therapy and to better study cysteine oxidations, we develop cysteine-reactive probes, N-acryloylindole-alkynes (NAIAs), which have superior cysteine reactivity owing to delocalization of π electrons of the acrylamide warhead over the whole indole scaffold. This allows NAIAs to probe functional cysteines more effectively than conventional iodoacetamide-alkyne, and to image oxidized thiols by confocal fluorescence microscopy. In mass spectrometry experiments, NAIAs successfully capture new oxidized cysteines, as well as a new pool of ligandable cysteines and proteins. Competitive activity-based protein profiling experiments further demonstrate the ability of NAIA to discover lead compounds targeting these cysteines and proteins. We show the development of NAIAs with activated acrylamide for advancing proteome-wide profiling and imaging ligandable cysteines and oxidized thiols.
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Affiliation(s)
- Tin-Yan Koo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Hinyuk Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Clive Yik-Sham Chung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong, P. R. China.
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37
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Kaur A, Lin W, Dovhalyuk V, Driutti L, Di Martino ML, Vujasinovic M, Löhr JM, Sellin ME, Globisch D. Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites. Chem Sci 2023; 14:5291-5301. [PMID: 37234898 PMCID: PMC10207876 DOI: 10.1039/d3sc00224a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/05/2023] [Indexed: 05/28/2023] Open
Abstract
Sulfur is an essential element of life. Thiol-containing metabolites in all organisms are involved in the regulation of diverse biological processes. Especially, the microbiome produces bioactive metabolites or biological intermediates of this compound class. The analysis of thiol-containing metabolites is challenging due to the lack of specific tools, making these compounds difficult to investigate selectively. We have now developed a new methodology comprising bicyclobutane for chemoselective and irreversible capturing of this metabolite class. We utilized this new chemical biology tool immobilized onto magnetic beads for the investigation of human plasma, fecal samples, and bacterial cultures. Our mass spectrometric investigation detected a broad range of human, dietary and bacterial thiol-containing metabolites and we even captured the reactive sulfur species cysteine persulfide in both fecal and bacterial samples. The described comprehensive methodology represents a new mass spectrometric strategy for the discovery of bioactive thiol-containing metabolites in humans and the microbiome.
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Affiliation(s)
- Amanpreet Kaur
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Weifeng Lin
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Vladyslav Dovhalyuk
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Léna Driutti
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
| | - Maria Letizia Di Martino
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Miroslav Vujasinovic
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
| | - J-Matthias Löhr
- Department for Digestive Diseases, Karolinska University Hospital Stockholm Sweden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institute Stockholm Sweden
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University 75123 Uppsala Sweden
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University 75124 Uppsala Sweden
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38
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Tyler JL, Aggarwal VK. Synthesis and Applications of Bicyclo[1.1.0]butyl and Azabicyclo[1.1.0]butyl Organometallics. Chemistry 2023; 29:e202300008. [PMID: 36786481 PMCID: PMC10947034 DOI: 10.1002/chem.202300008] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/15/2023]
Abstract
The use of metalated (aza)bicyclo[1.1.0]butanes in synthesis is currently experiencing a renaissance, as evidenced by the numerous reports in the last 5 years that have relied on such intermediates to undergo unique transformations or generate novel fragments. Since their discovery, these species have been demonstrated to participate in a wide range of reactions with carbon and heteroatom electrophiles, as well as metal complexes, to facilitate the rapid diversification of (aza)bicyclo[1.1.0]butane-containing compounds. Key to this is the relative acidity of the bridgehead C-H bonds which promotes facile deprotonation and subsequent functionalization of an unsubstituted position on the carbon framework via the intermediacy of a metalated (aza)bicyclo[1.1.0]butane. Additionally, the late-stage incorporation of deuterium atoms in strained fragments has led to the elucidation of numerous reaction mechanisms that involve strained bicycles. The continued investigation into the inimitable reactivity of metalated bicycles will cement their importance within the field of organometallic chemistry.
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Affiliation(s)
- Jasper L. Tyler
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
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39
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Ahmad R, Tyryshkin AM, Xie L, Hansen WA, Yachnin BJ, Emge TJ, Mashrai A, Khare SD, Knapp S. A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly. J Inorg Biochem 2023; 244:112206. [PMID: 37030124 DOI: 10.1016/j.jinorgbio.2023.112206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu++ and Zn++ in bidentate (N2) and tridentate (N2S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn++, Cu++, and Co++. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H2O/HO-, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.
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Affiliation(s)
- Raheel Ahmad
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Alexei M Tyryshkin
- Department of Marine and Coastal Sciences, Rutgers The State University of New Jersey, 71 Dudley Road, New Brunswick, NJ 08901, United States of America
| | - Lingjun Xie
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - William A Hansen
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Brahm J Yachnin
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Thomas J Emge
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America
| | - Ashraf Mashrai
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Sagar D Khare
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America; Rutgers Center for Integrative Proteomics Research, 174 Frelinghuysen Rd, Piscataway, NJ 08854, United States of America
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers The State University of New Jersey, 123 Bevier Rd, Piscataway, NJ 08854, United States of America.
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40
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Lv S, Xu F, Fan Y, Ding K, Li Z. Cyclopropenone, Cyclopropeniminium Ion, and Cyclopropenethione as Novel Electrophilic Warheads for Potential Target Discovery of Triple-Negative Breast Cancer. J Med Chem 2023; 66:2851-2864. [PMID: 36762554 DOI: 10.1021/acs.jmedchem.2c01889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Because very few targets are currently available for drug development, triple-negative breast cancer (TNBC) has been defined as one of the most difficult diseases for chemotherapy. Herein, we describe a suite of novel electrophilic warheads, which we have used in chemical proteomics studies in a search for potential targets for TNBC. Binding site analysis revealed that these warheads can modify not only highly nucleophilic residues, including cysteine and lysine, but also weakly nucleophilic residues. Cys12 of Kirsten rat sarcoma (KRASG12C) was successfully labeled by cyclopropenone and the cyclopropeniminium ions. Moderate inhibitory activity against TNBC cells was achieved with these novel electrophile-based probes. Activity-based protein profiling reveals that these electrophiles can covalently label a series of essential protein targets, including ALDH2, LRPPRC, and FABP5 from MDA-MB-231 cells. Further functional validation experiments demonstrated that FABP5 might be a potential target for TNBC.
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Affiliation(s)
- Shumin Lv
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Youlong Fan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
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41
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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42
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Kano K, Noda S, Sato S, Kuwata K, Mishiro‐Sato E. An efficient in‐gel digestion method on small amounts of protein sample from large intact gel pieces. SEPARATION SCIENCE PLUS 2023. [DOI: 10.1002/sscp.202200121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Keiko Kano
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Saki Noda
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Shinya Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Keiko Kuwata
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
| | - Emi Mishiro‐Sato
- Molecular Structure Center, Institute of Transformative Bio‐Molecules (WPI‐ITbM) Nagoya University Nagoya Japan
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43
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Pickford HD, Ripenko V, McNamee RE, Holovchuk S, Thompson AL, Smith RC, Mykhailiuk PK, Anderson EA. Rapid and Scalable Halosulfonylation of Strain-Release Reagents. Angew Chem Int Ed Engl 2023; 62:e202213508. [PMID: 36226350 PMCID: PMC10100009 DOI: 10.1002/anie.202213508] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 11/12/2022]
Abstract
Sulfonylated aromatics are commonplace motifs in drugs and agrochemicals. However, methods for the direct synthesis of sulfonylated non-classical arene bioisosteres, which could improve the physicochemical properties of drug and agrochemical candidates, are limited. Here we report a solution to this challenge: a one-pot halosulfonylation of [1.1.1]propellane, [3.1.1]propellane and bicyclo[1.1.0]butanes that proceeds under practical, scalable and mild conditions. The sulfonyl halides used in this chemistry feature aryl, heteroaryl and alkyl substituents, and are conveniently generated in situ from readily available sulfinate salts and halogen atom sources. This methodology enables the synthesis of an array of pharmaceutically and agrochemically relevant halogen/sulfonyl-substituted bioisosteres and cyclobutanes, on up to multidecagram scale.
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Affiliation(s)
- Helena D. Pickford
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Vasyl Ripenko
- Enamine LtdChervonotkatska 7802094KyivUkraine
- Chemistry DepartmentTaras Shevchenko National University of KyivVolodymyrska 6401601KyivUkraine
| | - Ryan E. McNamee
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Amber L. Thompson
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Russell C. Smith
- AbbVie Drug Discovery Science & Technology (DDST)1 North Waukegan RoadNorth ChicagoIL 60064USA
| | | | - Edward A. Anderson
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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44
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Bicyclobutanes as unusual building blocks for complexity generation in organic synthesis. Commun Chem 2023; 6:9. [PMID: 36697911 PMCID: PMC9837078 DOI: 10.1038/s42004-022-00811-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/28/2022] [Indexed: 01/13/2023] Open
Abstract
Bicyclobutanes are among the most highly strained isolable organic compounds and their associated low activation barriers to reactivity make them intriguing building-blocks in organic chemistry. In recent years, numerous creative synthetic strategies exploiting their heightened reactivity have been presented and these discoveries have often gone hand-in-hand with the development of more practical routes for their synthesis. Their proclivity as strain-release reagents through their weak central C-C bond has been harnessed in a variety of addition, rearrangement and insertion reactions, providing rapid access to a rich tapestry of complex molecular scaffolds. This review will provide an overview of the different options available for bicyclobutane synthesis, the main classes of compounds that can be prepared from bicyclobutanes, and the associated modes of reactivity used.
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45
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Livingstone K, Siebold K, Meyer S, Martín-Heras V, Daniliuc CG, Gilmour R. Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes. ACS Catal 2022; 12:14507-14516. [PMID: 36504915 PMCID: PMC9724094 DOI: 10.1021/acscatal.2c04511] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational no → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.
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46
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Abstract
We report the first palladium hydride enabled hydroalkenylation of strained molecules. This new mild protocol proceeds via a regio- and chemoselective hydropalladation step, followed by a photoinduced radical alkyl Heck reaction. This methodology represents a new reactivity mode for strained molecules and opens new avenues for photoinduced palladium catalysis. The reaction is compatible with a wide range of functional groups and can be applied to complex structures, delivering a diverse array of highly valuable and modifiable alkenylated cyclobutanes and cyclopropanes. A hydroalkenylation/diastereoselective rearrangement cascade toward a cyclopentene scaffold has also been demonstrated.
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Affiliation(s)
- Ziyan Zhang
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080-3021, United States
| | - Vladimir Gevorgyan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080-3021, United States
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47
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Covalent Warheads Targeting Cysteine Residue: The Promising Approach in Drug Development. Molecules 2022; 27:molecules27227728. [PMID: 36431829 PMCID: PMC9694382 DOI: 10.3390/molecules27227728] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/12/2022] Open
Abstract
Cysteine is one of the least abundant amino acids in proteins of many organisms, which plays a crucial role in catalysis, signal transduction, and redox regulation of gene expression. The thiol group of cysteine possesses the ability to perform nucleophilic and redox-active functions that are not feasible for other natural amino acids. Cysteine is the most common covalent amino acid residue and has been shown to react with a variety of warheads, especially Michael receptors. These unique properties have led to widespread interest in this nucleophile, leading to the development of a variety of cysteine-targeting warheads with different chemical compositions. Herein, we summarized the various covalent warheads targeting cysteine residue and their application in drug development.
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48
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Frank N, Nugent J, Shire BR, Pickford HD, Rabe P, Sterling AJ, Zarganes-Tzitzikas T, Grimes T, Thompson AL, Smith RC, Schofield CJ, Brennan PE, Duarte F, Anderson EA. Synthesis of meta-substituted arene bioisosteres from [3.1.1]propellane. Nature 2022; 611:721-726. [PMID: 36108675 DOI: 10.1038/s41586-022-05290-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022]
Abstract
Small-ring cage hydrocarbons are popular bioisosteres (molecular replacements) for commonly found para-substituted benzene rings in drug design1. The utility of these cage structures derives from their superior pharmacokinetic properties compared with their parent aromatics, including improved solubility and reduced susceptibility to metabolism2,3. A prime example is the bicyclo[1.1.1]pentane motif, which is mainly synthesized by ring-opening of the interbridgehead bond of the strained hydrocarbon [1.1.1]propellane with radicals or anions4. By contrast, scaffolds mimicking meta-substituted arenes are lacking because of the challenge of synthesizing saturated isosteres that accurately reproduce substituent vectors5. Here we show that bicyclo[3.1.1]heptanes (BCHeps), which are hydrocarbons for which the bridgehead substituents map precisely onto the geometry of meta-substituted benzenes, can be conveniently accessed from [3.1.1]propellane. We found that [3.1.1]propellane can be synthesized on a multigram scale, and readily undergoes a range of radical-based transformations to generate medicinally relevant carbon- and heteroatom-substituted BCHeps, including pharmaceutical analogues. Comparison of the absorption, distribution, metabolism and excretion (ADME) properties of these analogues reveals enhanced metabolic stability relative to their parent arene-containing drugs, validating the potential of this meta-arene analogue as an sp3-rich motif in drug design. Collectively, our results show that BCHeps can be prepared on useful scales using a variety of methods, offering a new surrogate for meta-substituted benzene rings for implementation in drug discovery programmes.
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Affiliation(s)
- Nils Frank
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeremy Nugent
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Bethany R Shire
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Helena D Pickford
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Alistair J Sterling
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tryfon Zarganes-Tzitzikas
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Thomas Grimes
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Russell C Smith
- Abbvie Drug Discovery Science & Technology (DDST), North Chicago, IL, USA
| | | | - Paul E Brennan
- Alzheimer's Research UK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford, UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Edward A Anderson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
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49
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Kelly CB, Milligan JA, Tilley LJ, Sodano TM. Bicyclobutanes: from curiosities to versatile reagents and covalent warheads. Chem Sci 2022; 13:11721-11737. [PMID: 36320907 PMCID: PMC9580472 DOI: 10.1039/d2sc03948f] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/24/2022] [Indexed: 09/16/2023] Open
Abstract
The unique chemistry of small, strained carbocyclic systems has long captivated organic chemists from a theoretical and fundamental standpoint. A resurgence of interest in strained carbocyclic species has been prompted by their potential as bioisosteres, high fraction of sp3 carbons, and limited appearance in the patent literature. Among strained ring systems, bicyclo[1.1.0]butane (BCB) stands apart as the smallest bicyclic carbocycle and is amongst the most strained carbocycles known. Despite the fact that BCBs have been synthesized and studied for well over 50 years, they have long been regarded as laboratory curiosities. However, new approaches for preparing, functionalizing, and using BCBs in "strain-release" transformations have positioned BCBs to be powerful synthetic workhorses. Further, the olefinic character of the bridgehead bond enables BCBs to be elaborated into various other ring systems and function as covalent warheads for bioconjugation. This review will discuss the recent developments in the synthesis and functionalization of BCBs as well as the applications of these strained rings in synthesis and drug discovery. An overview of the properties and the historical context of this interesting structure will be provided.
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Affiliation(s)
- Christopher B Kelly
- Discovery Process Research, Janssen Research & Development LLC 1400 McKean Road, Spring House PA 19477 USA
| | - John A Milligan
- Department of Biological and Chemical Sciences, College of Life Sciences, Thomas Jefferson University 4201 Henry Avenue Philadelphia PA 19144 USA
| | - Leon J Tilley
- Department of Chemistry, Stonehill College 320 Washington Street Easton MA 02357 USA
| | - Taylor M Sodano
- Therapeutics Discovery, Janssen Research & Development LLC 1400 McKean Road, Spring House PA 19477 USA
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Li S, Zhang P, Xu F, Hu S, Liu J, Tan Y, Tu Z, Sun H, Zhang ZM, He QY, Sun P, Ding K, Li Z. Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem 2022; 65:10408-10418. [PMID: 35880853 DOI: 10.1021/acs.jmedchem.2c00272] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covalent inhibitors with an electrophilic warhead have received considerable attention due to their remarkable pharmacological properties. However, the electrophilic warhead in covalent drugs is often an α, β-unsaturated amide, and the targets are mainly cysteine or lysine residues. Thus, the development of novel electrophiles that can target other amino acids is highly desirable. Ynamide, a useful and versatile building block, is commonly employed in the construction of various compounds in organic synthesis. The performance of this functional group in a proteome-wide environment has been studied here for the first time, and it has been shown that it can efficiently modify carboxyl residues in situ and in vitro. Upon incorporation of this ynamide warhead into the pharmacophores of kinase inhibitors, the resulting compound showed moderate inhibition against the EGFR L858R mutant but not against EGFR WT. This novel electrophilic group can be used in the development of new types of covalent inhibitors.
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Affiliation(s)
- Shengrong Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Pengwei Zhang
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, Guangdong, China
| | - Fang Xu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Shengcao Hu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Jiacong Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Yi Tan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengchao Tu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Qing-Yu He
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
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