1
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Mukherjee A, Kadam VD, Miao Q, Zhang W, MacKenzie KR, Tan Z, Teng M. On-demand modular assembly for expedited PROTAC development. Expert Opin Drug Discov 2024; 19:769-772. [PMID: 38842359 DOI: 10.1080/17460441.2024.2364637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Ayan Mukherjee
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Vilas D Kadam
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Qi Miao
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Wanheng Zhang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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2
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Abstract
Organoboron acids are stable, organic-soluble Lewis acids with potential application as catalysts for a wide variety of chemical reactions. In this review, we summarize the utility of boronic and borinic acids, as well as boric acid, as catalysts for organic transformations. Typically, the catalytic processes exploit the Lewis acidity of trivalent boron, enabling the reversible formation of a covalent bond with oxygen. Our focus is on recent developments in the catalysis of dehydration, carbonyl condensation, acylation, alkylation, and cycloaddition reactions. We conclude that organoboron acids have a highly favorable prospectus as the source of new catalysts.
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Affiliation(s)
- Brian J Graham
- Department of Chemistry, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Doyduk D, Derkus B, Sari B, Eylem CC, Nemutlu E, Yıldırır Y. Molecular docking, synthesis, anticancer activity, and metabolomics study of boronic acid ester-containing fingolimod derivatives. Arch Pharm (Weinheim) 2023; 356:e2300382. [PMID: 37768844 DOI: 10.1002/ardp.202300382] [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: 07/14/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/30/2023]
Abstract
In recent years, drugs that contain boronic acid groups, such as ixazomib (Ninlaro™) and bortezomib (Velcade™), have been used in the treatment of bone marrow cancer. The activity of compounds has been found to increase with the addition of boron atoms to the structure. In addition to these compounds, studies have found that fingolimod (FTY720) is more effective against breast cancer than cisplatin. Therefore, in this study, the first examples of boron-containing derivatives of fingolimod were designed and synthesized; in addition, their structures were confirmed by spectroscopic techniques. The synthesized boron-containing drug candidates were found to significantly inhibit cell proliferation and induce apoptosis-mediated cell death in HT-29 (colorectal cells), SaOs-2 (osteosarcoma cells), and U87-MG (glioblastoma cells). Moreover, we revealed that the anticancer effects of boron-containing fingolimod compounds were found to be significantly enhanced over boron-free control groups and, strikingly, over the widely used anticancer drug 5-fluorouracil. The metabolomic analysis confirmed that administration of the boron-containing drug candidates induces significant changes in the metabolite profiles in HT-29, SaOs-2, and U87-MG cells. Altogether, our results showed that boron-containing fingolimod compounds can be further examined to reveal their potential as anticancer drug candidates.
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Affiliation(s)
- Doğukan Doyduk
- Department of Chemistry, Faculty of Science, Gazi University, Ankara, Turkey
| | - Burak Derkus
- Stem Cell Research Lab, Department of Chemistry, Faculty of Science, Ankara University, Ankara, Turkey
| | - Buse Sari
- Stem Cell Research Lab, Department of Chemistry, Faculty of Science, Ankara University, Ankara, Turkey
| | - Cemil Can Eylem
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Emirhan Nemutlu
- Analytical Chemistry Division, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
- Bioanalytic and Omics Laboratory, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Yılmaz Yıldırır
- Department of Chemistry, Faculty of Science, Gazi University, Ankara, Turkey
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4
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van der Zouwen AJ, Jeucken A, van der Pol E, Boerema G, Slotboom DJ, Witte MD. The linkage-type and the exchange molecule affect the protein-labeling efficiency of iminoboronate probes. Org Biomol Chem 2023; 21:9173-9181. [PMID: 37947354 PMCID: PMC10686633 DOI: 10.1039/d3ob01269g] [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: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Reversible bioorthogonal conjugation reactions have been exploited in the chemoproteomic field to prepare protein labeling reagents and to visualize labeled proteins. We recently demonstrated that reversible iminoboronates can be used to prepare probes from fragment libraries and that the linkage subsequently can be used to detect the labeled proteins. In this study, we determined the effect of the stability of the iminoboronate linkage on the efficiency of the labeling protocol. Our study reveals that the linkage should be stable enough to allow for efficient targeting, but should be labile enough to detect the labeled protein. Acyl hydrazides were identified as the most suitable handles for the probe synthesis step. Anthranilic hydrazides and N-hydroxy semicarbazides were found to be the most efficient read-out molecules. With these novel exchange molecules, native probe-labeled proteins could be visualized under physiological conditions.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Aike Jeucken
- Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
| | - Elske van der Pol
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Gerben Boerema
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Dirk J Slotboom
- Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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5
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Gui W, Giardina SF, Balzarini M, Barany F, Kodadek T. Reversible Assembly of Proteolysis Targeting Chimeras. ACS Chem Biol 2023; 18:1582-1593. [PMID: 37422908 DOI: 10.1021/acschembio.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are of significant current interest for the development of probe molecules and drug leads. However, they suffer from certain limitations. PROTACs are rule-breaking molecules with sub-optimal cellular permeability, solubility, and other drug-like properties. In particular, they exhibit an unusual dose-response curve where high concentrations of the bivalent molecule inhibit degradation activity, a phenomenon known as the hook effect. This will likely complicate their use in vivo. In this study, we explore a novel approach to create PROTACs that do not exhibit a hook effect. This is achieved by equipping the target protein and E3 ubiquitin ligase ligands with functionalities that undergo rapid and reversible covalent assembly in cellulo. We report the development of Self-Assembled Proteolysis Targeting Chimeras that mediate the degradation of the Von Hippel-Lindau E3 ubiquitin ligase and do not evince a hook effect.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Madeline Balzarini
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Thomas Kodadek
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, 120 Scripps Way, Jupiter, Florida 33458, United States
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6
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Gless BH, Schmied SH, Bejder BS, Olsen CA. Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation. JACS AU 2023; 3:1443-1451. [PMID: 37234128 PMCID: PMC10207088 DOI: 10.1021/jacsau.3c00095] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.
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7
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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8
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Mitry MMA, Greco F, Osborn HMI. In Vivo Applications of Bioorthogonal Reactions: Chemistry and Targeting Mechanisms. Chemistry 2023; 29:e202203942. [PMID: 36656616 DOI: 10.1002/chem.202203942] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Bioorthogonal chemistry involves selective biocompatible reactions between functional groups that are not normally present in biology. It has been used to probe biomolecules in living systems, and has advanced biomedical strategies such as diagnostics and therapeutics. In this review, the challenges and opportunities encountered when translating in vitro bioorthogonal approaches to in vivo settings are presented, with a focus on methods to deliver the bioorthogonal reaction components. These methods include metabolic bioengineering, active targeting, passive targeting, and simultaneously used strategies. The suitability of bioorthogonal ligation reactions and bond cleavage reactions for in vivo applications is critically appraised, and practical considerations such as the optimum scheduling regimen in pretargeting approaches are discussed. Finally, we present our own perspectives for this area and identify what, in our view, are the key challenges that must be overcome to maximise the impact of these approaches.
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Affiliation(s)
- Madonna M A Mitry
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK.,Department of Pharmaceutical Chemistry Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Francesca Greco
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading Whiteknights, Reading, RG6 6AD, UK
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9
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Rose NC, Sanchez AV, Tipple EF, Lynam JM, Spicer CD. Insight into ortho-boronoaldehyde conjugation via a FRET-based reporter assay. Chem Sci 2022; 13:12791-12798. [PMID: 36519041 PMCID: PMC9645387 DOI: 10.1039/d2sc04574e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2023] Open
Abstract
Ortho-boronoaldehydes react with amine-based nucleophiles with dramatically increased rates and product stabilities, relative to unfunctionalised benzaldehydes, leading to exciting applications across biological and material chemistry. We have developed a novel Förster resonance energy transfer (FRET)-based assay to provide key new insights into the reactivity of these boronoaldehydes, allowing us to track conjugation with unprecedented sensitivity and accuracy under standardised conditions. Our results highlight the key role played by reaction pH, buffer additives, and boronoaldehyde structure in controlling conjugation speed and stability, providing design criteria for further innovations and applications in the field.
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Affiliation(s)
- Nicholas C Rose
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
| | - Anaïs V Sanchez
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
| | - Eve F Tipple
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
| | - Jason M Lynam
- Department of Chemistry, University of York Heslington YO10 5DD UK
| | - Christopher D Spicer
- Department of Chemistry, University of York Heslington YO10 5DD UK
- York Biomedical Research Institute, University of York Heslington YO10 5DD UK
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10
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Kondengadan SM, Bansal S, Yang C, Liu D, Fultz Z, Wang B. Click chemistry and drug delivery: A bird’s-eye view. Acta Pharm Sin B 2022; 13:1990-2016. [DOI: 10.1016/j.apsb.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/12/2022] [Accepted: 10/12/2022] [Indexed: 11/01/2022] Open
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11
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Zhao H, Shan A, Liang Y, Wu H, He Y, Chen H, Zeng J, Gu J, Song JP, Qiu H, Zhang J. Boron-Assisted Selective Citrulline Modification under Mild Conditions. Org Lett 2022; 24:6351-6355. [PMID: 35997298 DOI: 10.1021/acs.orglett.2c02722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein citrullination is one type of protein post-translational modification. Previous methods entail the use of a strongly acidic condition (pH <1), which impedes its exploration under physiological and pathological conditions. Here, we developed a biocompatible method based on o-boron-assisted citrulline modification. We demonstrated that this method enables selective and mainly irreversible modification of citrulline residues under neutral conditions. We expect that it will provide a valuable tool for the study of protein citrullination.
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Affiliation(s)
- Hailong Zhao
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Aidong Shan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yunshi Liang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Haiting Wu
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yiting He
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Huihong Chen
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiaxin Zeng
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, China
| | - Jiangyong Gu
- Research Centre for Integrative Medicine, School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jian-Ping Song
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Hong Qiu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Zhang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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12
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António JPM, Carvalho JI, André AS, Dias JNR, Aguiar SI, Faustino H, Lopes RMRM, Veiros LF, Bernardes GJL, Silva FA, Gois PMP. Diazaborines Are a Versatile Platform to Develop ROS‐Responsive Antibody Drug Conjugates**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- João P. M. António
- Research Institute for Medicines (iMed.ULisboa) Faculdade de Farmácia Universidade de Lisboa Av. Prof. Gama Pinto 1649-003 Lisboa Portugal
| | - Joana Inês Carvalho
- Research Institute for Medicines (iMed.ULisboa) Faculdade de Farmácia Universidade de Lisboa Av. Prof. Gama Pinto 1649-003 Lisboa Portugal
| | - Ana S. André
- Centro de Investigação Interdisciplinar em Sanidade Animal Faculdade de Medicina Veterinária Universidade de Lisboa Av. Universidade Técnica 1300-477 Lisboa Portugal
| | - Joana N. R. Dias
- Centro de Investigação Interdisciplinar em Sanidade Animal Faculdade de Medicina Veterinária Universidade de Lisboa Av. Universidade Técnica 1300-477 Lisboa Portugal
| | - Sandra I. Aguiar
- Centro de Investigação Interdisciplinar em Sanidade Animal Faculdade de Medicina Veterinária Universidade de Lisboa Av. Universidade Técnica 1300-477 Lisboa Portugal
| | - Hélio Faustino
- Research Institute for Medicines (iMed.ULisboa) Faculdade de Farmácia Universidade de Lisboa Av. Prof. Gama Pinto 1649-003 Lisboa Portugal
| | - Ricardo M. R. M. Lopes
- Research Institute for Medicines (iMed.ULisboa) Faculdade de Farmácia Universidade de Lisboa Av. Prof. Gama Pinto 1649-003 Lisboa Portugal
| | - Luis F. Veiros
- Centro de Química Estrutural and Departamento de Engenharia Química Instituto Superior Técnico Universidade de Lisboa Av. Rovisco Pais 1 1049-001 Lisboa Portugal
| | - Gonçalo J. L. Bernardes
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CB2 1EW Cambridge United Kingdom
| | - Frederico A. Silva
- Centro de Investigação Interdisciplinar em Sanidade Animal Faculdade de Medicina Veterinária Universidade de Lisboa Av. Universidade Técnica 1300-477 Lisboa Portugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa) Faculdade de Farmácia Universidade de Lisboa Av. Prof. Gama Pinto 1649-003 Lisboa Portugal
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13
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António JPM, Carvalho JI, André AS, Dias JNR, Aguiar SI, Faustino H, Lopes RMRM, Veiros LF, Bernardes GJL, da Silva FA, Gois PMP. Diazaborines Are a Versatile Platform to Develop ROS-Responsive Antibody Drug Conjugates*. Angew Chem Int Ed Engl 2021; 60:25914-25921. [PMID: 34741376 DOI: 10.1002/anie.202109835] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Indexed: 12/11/2022]
Abstract
Antibody-drug conjugates (ADCs) are a new class of therapeutics that combine the lethality of potent cytotoxic drugs with the targeting ability of antibodies to selectively deliver drugs to cancer cells. In this study we show for the first time the synthesis of a reactive-oxygen-species (ROS)-responsive ADC (VL-DAB31-SN-38) that is highly selective and cytotoxic to B-cell lymphoma (CLBL-1 cell line, IC50 value of 54.1 nM). The synthesis of this ADC was possible due to the discovery that diazaborines (DABs) are a very effective ROS-responsive unit that are also very stable in buffer and in plasma. DFT calculations performed on this system revealed a favorable energetic profile (ΔGR=-74.3 kcal mol-1 ) similar to the oxidation mechanism of aromatic boronic acids. DABs' very fast formation rate and modularity enabled the construction of different ROS-responsive linkers featuring self-immolative modules, bioorthogonal functions, and bioconjugation handles. These structures were used in the site-selective functionalization of a VL antibody domain and in the construction of the homogeneous ADC.
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Affiliation(s)
- João P M António
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Joana Inês Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Ana S André
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Joana N R Dias
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Sandra I Aguiar
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Hélio Faustino
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Ricardo M R M Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Luis F Veiros
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001, Lisboa, Portugal
| | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Frederico A da Silva
- Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Pedro M P Gois
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
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14
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Cai P, Schneider LA, Stress C, Gillingham D. Building Boron Heterocycles into DNA-Encoded Libraries. Org Lett 2021; 23:8772-8776. [PMID: 34723549 DOI: 10.1021/acs.orglett.1c03262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA-encoded library (DEL) technology uses DNA tags to track the synthetic history of individual members in a split-and-pool combinatorial synthesis scheme. DEL synthesis hinges on robust methodologies that tolerate combinatorial synthesis schemes while not destroying the information in DNA. We introduce here a DEL-compatible reaction that assembles a boron-containing pyridazine heterocycle. The heterocycle is unique because it can engage in reversible covalent interactions with alcohols─a feature that, until now, has not been deliberately engineered into DELs.
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Affiliation(s)
- Pinwen Cai
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Lukas A Schneider
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Cedric Stress
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel 4056, Switzerland
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15
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Kocsis I, Ding Y, Williams NH, Hunter CA. Transmembrane signal transduction by cofactor transport. Chem Sci 2021; 12:12377-12382. [PMID: 34603667 PMCID: PMC8480319 DOI: 10.1039/d1sc03910e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/17/2021] [Indexed: 11/30/2022] Open
Abstract
Information processing and cell signalling in biological systems relies on passing chemical signals across lipid bilayer membranes, but examples of synthetic systems that can achieve this process are rare. A synthetic transducer has been developed that triggers catalytic hydrolysis of an ester substrate inside lipid vesicles in response to addition of metal ions to the external vesicle solution. The output signal generated in the internal compartment of the vesicles is produced by binding of a metal ion cofactor to a head group on the transducer to form a catalytically competent complex. The mechanism of signal transduction is based on transport of the metal ion cofactor across the bilayer by the transducer, and the system can be reversibly switched between on and off states by adding cadmium(ii) and ethylene diamine tetracarboxylic acid input signals respectively. The transducer is also equipped with a hydrazide moiety, which allows modulation of activity through covalent conjugation with aldehydes. Conjugation with a sugar derivative abolished activity, because the resulting hydrazone is too polar to cross the bilayer, whereas conjugation with a pyridine derivative increased activity. Coupling transport with catalysis provides a straightforward mechanism for generating complex systems using simple components. Synthetic transducers transport externally added metal ion cofactors across the lipid bilayer membrane of vesicles to trigger catalysis of ester hydrolysis in the inner compartment. Signal transduction activity is modulated by hydrazone formation.![]()
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Affiliation(s)
- Istvan Kocsis
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yudi Ding
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | | | - Christopher A Hunter
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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16
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Han GS, Domaille DW. Tuning the exchange dynamics of boronic acid hydrazones and oximes with pH and redox control. Org Biomol Chem 2021; 19:4986-4991. [PMID: 34008683 DOI: 10.1039/d1ob00191d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Dynamic bonds continually form and dissociate at equilibrium. Carbonyl compounds with proximal boronic acids, including 2-formylphenylboronic acid (2-FPBA), have been reported to form highly dynamic covalent hydrazone and oxime bonds in physiological conditions, but strategies to tune the dynamics have not yet been reported. Here, we characterize the dynamics of 2-FPBA-derived hydrazones and oximes and account for both the rapid rate of formation (∼102-103 M-1 s-1) and the relatively fast rate of hydrolysis (∼10-4 s-1) at physiological pH. We further show that these substrates undergo exchange with α-nucleophiles, which can be reversibly paused and restarted with pH control. Finally, we show that oxidation of the arylboronic acid effectively abolishes the rapid dynamics, which slows the forward reaction by more than 30 000 times and increases the hydrolytic half-life from 50 minutes to 6 months at physiological pH. These results set the stage to explore these linkages in dynamic combinatorial libraries, reversible bioconjugation, and self-healing materials.
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Affiliation(s)
- Gun Su Han
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA.
| | - Dylan W Domaille
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA.
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17
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van der Zouwen AJ, Witte MD. Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes. Front Chem 2021; 9:644811. [PMID: 33937194 PMCID: PMC8082414 DOI: 10.3389/fchem.2021.644811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial and modular methods to synthesize small molecule modulators of protein activity have proven to be powerful tools in the development of new drug-like molecules. Over the past decade, these methodologies have been adapted toward utilization in the development of activity- and affinity-based chemical probes, as well as in chemoproteomic profiling. In this review, we will discuss how methods like multicomponent reactions, DNA-encoded libraries, phage displays, and others provide new ways to rapidly screen novel chemical probes against proteins of interest.
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Affiliation(s)
- Antonie J van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
| | - Martin D Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen, Groningen, Netherlands
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18
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van der Zouwen AJ, Jeucken A, Steneker R, Hohmann KF, Lohse J, Slotboom DJ, Witte MD. Iminoboronates as Dual-Purpose Linkers in Chemical Probe Development. Chemistry 2021; 27:3292-3296. [PMID: 33259638 PMCID: PMC7898632 DOI: 10.1002/chem.202005115] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Indexed: 11/25/2022]
Abstract
Chemical probes that covalently modify proteins of interest are powerful tools for the research of biological processes. Important in the design of a probe is the choice of reactive group that forms the covalent bond, as it decides the success of a probe. However, choosing the right reactive group is not a simple feat and methodologies for expedient screening of different groups are needed. We herein report a modular approach that allows easy coupling of a reactive group to a ligand. α-Nucleophile ligands are combined with 2-formylphenylboronic acid derived reactive groups to form iminoboronate probes that selectively label their target proteins. A transimination reaction on the labeled proteins with an α-amino hydrazide provides further modification, for example to introduce a fluorophore.
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Affiliation(s)
| | - Aike Jeucken
- Membrane EnzymologyGroningen Biomolecular Sciences and Biotechnology Institute9747AGGroningenThe Netherlands
| | - Roy Steneker
- Chemical Biology IIStratingh Institute for ChemistryNijenborgh 79747 AGGroningenThe Netherlands
| | - Katharina F. Hohmann
- Chemical Biology IIStratingh Institute for ChemistryNijenborgh 79747 AGGroningenThe Netherlands
| | - Jonas Lohse
- Chemical Biology IIStratingh Institute for ChemistryNijenborgh 79747 AGGroningenThe Netherlands
| | - Dirk J. Slotboom
- Membrane EnzymologyGroningen Biomolecular Sciences and Biotechnology Institute9747AGGroningenThe Netherlands
| | - Martin D. Witte
- Chemical Biology IIStratingh Institute for ChemistryNijenborgh 79747 AGGroningenThe Netherlands
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19
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Groleau RR, James TD, Bull SD. The Bull-James assembly: Efficient iminoboronate complex formation for chiral derivatization and supramolecular assembly. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213599] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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António JPM, Faustino H, Gois PMP. A 2-formylphenylboronic acid (2FPBA)-maleimide crosslinker: a versatile platform for Cys-peptide-hydrazine conjugation and interplay. Org Biomol Chem 2021; 19:6221-6226. [PMID: 34198316 DOI: 10.1039/d1ob00917f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, we describe the preparation of a heterobifunctional 2-formylphenylboronic acid (2-FPBA)-maleimide crosslinker and explore its versatility in the preparation of various bioconjugates. We demonstrate the straightforward attachment of hydrazine payloads to cysteine residues in peptides, as well as the crosslinking of different thiol-bearing peptides or payloads with N-terminal cysteine peptides. Importantly, the dynamic nature of the 2-FPBA handle enables an interplay between the thiazolidine and diazaborine forms, which allows obtaining various products controlled by (and in some cases independent of) the order of addition of the components.
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Affiliation(s)
- João P M António
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal. and Chimie ParisTech, PSL University, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, F-75005 Paris, France
| | - Hélio Faustino
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal. and Association BLC3-Innovation and Technology Campus, Oliveira do Hospital, Portugal
| | - Pedro M P Gois
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
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21
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Chatterjee S, Anslyn EV, Bandyopadhyay A. Boronic acid based dynamic click chemistry: recent advances and emergent applications. Chem Sci 2020; 12:1585-1599. [PMID: 34163920 PMCID: PMC8179052 DOI: 10.1039/d0sc05009a] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/27/2020] [Indexed: 11/28/2022] Open
Abstract
Recently, reversible click reactions have found numerous applications in chemical biology, supramolecular chemistry, and biomedical applications. Boronic acid (BA)-mediated cis-diol conjugation is one of the best-studied reactions among them. An excellent understanding of the chemical properties and biocompatibility of BA-based compounds has inspired the exploration of novel chemistries using boron to fuel emergent sciences. This topical review focuses on the recent progress of iminoboronate and salicylhydroxamic-boronate constituted reversible click chemistries in the past decade. We highlight the mechanism of reversible kinetics and its applications in chemical biology, medicinal chemistry, biomedical devices, and material chemistry. This article also emphasizes the fundamental reactivity of these two conjugate chemistries with assorted nucleophiles at variable pHs, which is of utmost importance to any stimuli-responsive biological and material chemistry explorations.
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Affiliation(s)
- Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Punjab-781039 India
| | - Eric V Anslyn
- Department of Chemistry, University of Texas 1 University Station A1590 Austin Texas 78712 USA
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology Ropar Punjab-781039 India
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22
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Zhou Y, Piergentili I, Hong J, van der Helm MP, Macchione M, Li Y, Eelkema R, Luo S. Indoline Catalyzed Acylhydrazone/Oxime Condensation under Neutral Aqueous Conditions. Org Lett 2020; 22:6035-6040. [PMID: 32790427 DOI: 10.1021/acs.orglett.0c02128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Acylhydrazones formation has been widely applied in materials science and biolabeling. However, their sluggish condensation rate under neutral conditions limits its application. Herein, indolines with electron-donating groups are reported as a new catalyst scaffold, which can catalyze acylhydrazone, hydrazone, and oxime formation via an iminium ion intermediate. This new type of catalyst showed up to 15-fold rate enhancement over the traditional aniline-catalyzed reaction at neutral conditions. The identified indoline catalyst was successfully applied in hydrogel formation.
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Affiliation(s)
- Yuntao Zhou
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Irene Piergentili
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jennifer Hong
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Michelle P van der Helm
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Mariano Macchione
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Yao Li
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Sanzhong Luo
- Center of Basic Molecular Science (CBMS), Department of Chemistry, Tsinghua University, Beijing 100084, China
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23
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Nguyen SS, Prescher JA. Developing bioorthogonal probes to span a spectrum of reactivities. Nat Rev Chem 2020; 4:476-489. [PMID: 34291176 DOI: 10.1038/s41570-020-0205-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.
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Affiliation(s)
- Sean S Nguyen
- Departments of Chemistry, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States.,Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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24
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Chen H, Ye H, Hai Y, Zhang L, You L. n → π* interactions as a versatile tool for controlling dynamic imine chemistry in both organic and aqueous media. Chem Sci 2020; 11:2707-2715. [PMID: 34084329 PMCID: PMC8157614 DOI: 10.1039/c9sc05698j] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/31/2020] [Indexed: 11/21/2022] Open
Abstract
The imine bond holds a prominent place in supramolecular chemistry and materials science, and one issue is the stability of imines due to their electrophilic nature. Here we introduced ortho-carboxylate groups into a series of aromatic aldehydes/imines for dictating imine dynamic covalent chemistry (DCC) through n → π* interactions, one class of widespread and yet underused non-covalent interactions. The thermodynamically stabilizing role of carboxylate-aldehyde/imine n → π* interactions in acetonitrile was elucidated by the movement of the imine exchange equilibrium and further supported by crystal analysis. Computational studies provided mechanistic insights for n → π* interactions, the strength of which can surpass that of CH hydrogen bonding and is dependent on the orientation of interacting sites based on natural bond orbital analysis. Moreover, the substituent effect and the combination of recognition sites allowed additional means for modulation. Finally, to show the relevance of our findings ortho-carboxylate containing aldehydes were used to regulate imine formation/exchange in water, and modification of the N-terminus of amino acids and peptides was achieved in a neutral buffer. This work represents the latest example of weak interactions governing DCC and sets the stage for assembly and application studies.
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Affiliation(s)
- Hang Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ling Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences Fuzhou 350002 China
- University of Chinese Academy of Sciences Beijing 100049 China
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25
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Abstract
Click chemistry has found wide application in bioconjugation, enabling control over the site of modification in biomolecules. Demonstrations of this chemistry to construct chemically defined antibody-drug conjugates (ADCs) have increased in recent years, following studies that support benefits of homogeneity and site-specificity of drug placement on the antibody. In this chapter, a brief history of early applications of this chemistry in ADCs is presented. Examples of click chemistries that are utilized for ADC synthesis, including those currently undergoing clinical investigations, are enumerated. Protocols for two common conjugation methods based on carbonyl-aminooxy coupling and strain-promoted azide-alkyne cycloaddition are described.
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26
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Su D, Coste M, Diaconu A, Barboiu M, Ulrich S. Cationic dynamic covalent polymers for gene transfection. J Mater Chem B 2020; 8:9385-9403. [DOI: 10.1039/d0tb01836h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dynamic covalent polymers have revealed strong potential in gene delivery, thanks to their versatile self-assembly, adaptive and responsive behaviors.
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Affiliation(s)
- Dandan Su
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- University of Montpellier
- ENSCM
- CNRS
| | - Maëva Coste
- Institut des Biomolécules Max Mousseron (IBMM)
- CNRS
- Université of Montpellier
- ENSCM
- Montpellier
| | - Andrei Diaconu
- Petru Poni” Institute of Macromolecular Chemistry of Romanian Academy
- Iasi
- Romania
| | - Mihail Barboiu
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- University of Montpellier
- ENSCM
- CNRS
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- CNRS
- Université of Montpellier
- ENSCM
- Montpellier
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27
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He M, Lehn JM. Time-Dependent Switching of Constitutional Dynamic Libraries and Networks from Kinetic to Thermodynamic Distributions. J Am Chem Soc 2019; 141:18560-18569. [DOI: 10.1021/jacs.9b09395] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Meixia He
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
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28
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Gu H, Ghosh S, Staples RJ, Bane SL. β-Hydroxy-Stabilized Boron-Nitrogen Heterocycles Enable Rapid and Efficient C-Terminal Protein Modification. Bioconjug Chem 2019; 30:2604-2613. [PMID: 31483610 DOI: 10.1021/acs.bioconjchem.9b00534] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bioorthogonal chemistry has enabled the development of bioconjugates in physiological environments while averting interference from endogenous biomolecules. Reactions between carbonyl-containing molecules and alkoxyamines or hydrazines have experienced a resurgence in popularity in bioorthogonal chemistry owing to advances that allow the reactions to occur under physiological conditions. In particular, ortho-carbonyl-substituted phenylboronic acids (CO-PBAs) exhibit greatly accelerated rates of hydrazone and oxime formation via intramolecular Lewis acid catalysis. Unfortunately, the rate of the reverse reaction is also increased, yielding a kinetically less stable bioconjugate. When the substrate is a hydrazine derivative, an intramolecular reaction between the boronic acid and the hydrazone can lead to the formation of a heterocycle containing a boron-nitrogen bond. We have shown previously that α-amino hydrazides undergo rapid reaction with CO-PBAs to form highly stable, tricyclic products, and that this reaction is orthogonal to the popular azide-alkyne and tetrazine-alkene reactions. In this work, we explore a series of heteroatom-substituted hydrazides for their ability to form tricyclic products with two CO-PBAs, 2-formylphenylboronic acid (2fPBA), and 2-acetylphenylboronic acid (AcPBA). In particular, highly stable products were formed using β-hydroxy hydrazides and 2fPBA. C-Terminal β-hydroxy hydrazide proteins are available using conventional biochemical methods, which alleviates one of the difficulties with applications of bioorthogonal chemical reactions: site-specific incorporation of a reactive group into the biomolecular target. Using sortase-mediated ligation (SML), C-terminal threonine and serine hydrazides were appended to a model eGFP protein in high yield. Subsequent labeling with 2fPBA functionalized probes could be performed quickly and quantitatively at neutral pH using micromolar concentrations of reactants. The SML process was applied directly to an expressed protein in cellular extract, and the C-terminal modified target protein was selectively immobilized using 2fPBA-agarose. Elution from the agarose yielded a highly pure protein that retained the hydrazide functionality. This strategy should be generally applicable for rapid, efficient site-specific protein labeling, protein immobilization, and preparation of highly pure functionalized proteins.
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Affiliation(s)
- Han Gu
- Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States
| | - Saptarshi Ghosh
- Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States
| | - Richard J Staples
- Department of Chemistry and Chemical Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Susan L Bane
- Department of Chemistry , Binghamton University, State University of New York , Binghamton , New York 13902 , United States
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29
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Li K, Kelly MA, Gao J. Biocompatible conjugation of Tris base to 2-acetyl and 2-formyl phenylboronic acid. Org Biomol Chem 2019; 17:5908-5912. [PMID: 31145403 PMCID: PMC6581600 DOI: 10.1039/c9ob00726a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We describe the biocompatible conjugation of the Tris base to 2-formyl and 2-acetylphenylboronic acid (abbreviated as 2-FPBA and 2-APBA respectively), which have emerged as a versatile chemotype for fast biocompatible conjugation reactions. Tris base was found to react with 2-FPBA/APBA to give oxazolidinoboronate (OzB) complexes, analogous to the thiazolidinoboronate (TzB) and imidazolidinoboronate (IzB) complex formation that we recently reported. The Tris conjugations proceed well in complex biological media, and in contrast to the TzB/IzB complexes, the Tris conjugates exhibit superior kinetic stability (dissociation over days) as well as chemical stability against oxidation. We demonstrate the utility of such conjugation chemistries via a small molecule-induced peptide cyclization in blood serum.
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Affiliation(s)
- Kaicheng Li
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, USA.
| | - Michael A Kelly
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, USA.
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, USA.
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30
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Xu Y, Wang Y, Liu P, Chu GC, Xu H, Li YM, Wang J, Shi J. Catalyst free hydrazone ligation for protein labeling and modification using electron-deficient benzaldehyde reagents. Org Biomol Chem 2019; 16:7036-7040. [PMID: 30238118 DOI: 10.1039/c8ob01810c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bioorthogonal reactions have emerged as valuable tools for site-specific protein labeling and modification in vitro and in vivo. Hydrazone and oxime ligation has recently attracted considerable attention for wide applications in the conjugation of biomolecules. However, this kind of reaction has suffered from slow kinetics under physiological conditions and toxicity or complications of the reaction system due to catalysts. In this work we have developed an electron-deficient benzaldehyde reagent, which can be easily equipped with various types of bio-functional molecules for catalyst-free hydrazone ligation. The reagent can be equipped with not only small molecules such as fluorescence dyes or drugs, but also macromolecules like PEG. These can be precisely ligated to the C-terminus of proteins by an efficient hydrazone reaction at neutral pH and room temperature. The new reagent based catalyst-free hydrazone ligation provides a practical approach for the site specific modification of proteins.
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Affiliation(s)
- Yang Xu
- School of Biological and Medical Engineering, Hefei University of Technology, Hefei 230009, P. R. China.
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31
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António JPM, Russo R, Carvalho CP, Cal PMSD, Gois PMP. Boronic acids as building blocks for the construction of therapeutically useful bioconjugates. Chem Soc Rev 2019; 48:3513-3536. [DOI: 10.1039/c9cs00184k] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes boronic acid's contribution to the development of bioconjugates with a particular focus on the molecular mechanisms underlying its role in the construction and function of the bioconjugate, namely as a bioconjugation warhead, as a payload and as part of a bioconjugate linker.
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Affiliation(s)
- João P. M. António
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Roberto Russo
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Cátia Parente Carvalho
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Pedro M. S. D. Cal
- Instituto de Medicina Molecular
- Faculty of Medicine
- Universidade de Lisboa
- Lisbon
- Portugal
| | - Pedro M. P. Gois
- Research Institute for Medicines (iMed.ULisboa)
- Faculty of Pharmacy
- Universidade de Lisboa
- Lisbon
- Portugal
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32
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Parmar S, Pawar SP, Iyer R, Kalia D. Aldehyde-mediated bioconjugation via in situ generated ylides. Chem Commun (Camb) 2019; 55:14926-14929. [DOI: 10.1039/c9cc07443k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a technically simple approach for rapid, high-yielding and site-selective aldehyde-mediated bioconjugation for protein labelling and cellular applications.
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Affiliation(s)
- Sangeeta Parmar
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal 462066
- India
| | - Sharad P. Pawar
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal 462066
- India
| | - Ramkumar Iyer
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal 462066
- India
| | - Dimpy Kalia
- Department of Chemistry
- Indian Institute of Science Education and Research (IISER) Bhopal
- Bhopal 462066
- India
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33
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Akgun B, Hall DG. Boronic Acids as Bioorthogonal Probes for Site‐Selective Labeling of Proteins. Angew Chem Int Ed Engl 2018; 57:13028-13044. [DOI: 10.1002/anie.201712611] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/23/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Dennis G. Hall
- Department of Chemistry—CCIS 4–010University of Alberta Edmonton Alberta T6G 2G2 Canada
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34
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Cambray S, Gao J. Versatile Bioconjugation Chemistries of ortho-Boronyl Aryl Ketones and Aldehydes. Acc Chem Res 2018; 51:2198-2206. [PMID: 30110146 DOI: 10.1021/acs.accounts.8b00154] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biocompatible and bioorthogonal conjugation reactions have proven to be powerful tools in biological research and medicine. While the advent of bioorthogonal conjugation chemistries greatly expands our capacity to interrogate specific biomolecules in situ, biocompatible reactions that target endogenous reactive groups have given rise to a number of covalent drugs as well as a battery of powerful research tools. Despite the impressive progress, limitations do exist with the current conjugation chemistries. For example, most known bioorthogonal conjugations suffer from slow reaction rates and imperfect bioorthogonality. On the other hand, covalent drugs often display high toxicity due to off-target labeling and immunogenicity. These limitations demand continued pursuit of conjugation chemistries with optimal characteristics for biological applications. A spate of papers appearing in recent literature report the conjugation chemistries of 2-formyl and 2-acetyl phenylboronic acids (abbreviated as 2-FPBA and 2-APBA, respectively). These simple reactants are found to undergo fast conjugation with various nucleophiles under physiological conditions, showing great promise for biological applications. The versatile reactivity of 2-FPBA and 2-APBA manifests in dynamic conjugation with endogenous nucleophiles as well as conjugation with designer nucleophiles in a bioorthogonal manner. 2-FPBA/APBA conjugates with amines in biomolecules, such as lysine side chains and aminophospholipids, in a highly dynamic manner to give iminoboronates. In contrast to typical imines, iminoboronates enjoy much improved thermodynamic stability, yet are kinetically labile for hydrolysis due to imine activation by the boronic acid. Dynamic conjugations as such present a novel binding mechanism analogous to hydrogen bonding and electrostatic interactions. Implementation of this covalent binding mechanism has yielded reversible covalent probes of prevalent bacterial pathogens. It has also resulted in reversible covalent inhibitors of a therapeutically important protein Mcl-1. Such covalent probes/inhibitors with 2-FPBA/APBA warheads avoid permanent modification of their biological target, potentially able to mitigate off-target labeling and immunogenicity of covalent drugs. The dynamic conjugation of 2-FPBA/APBA has been recently extended to N-terminal cysteines, which can be selectively targeted via formation of a thiazolidino boronate (TzB) complex. The dynamic TzB formation expands the toolbox for site-specific protein labeling and the development of covalent drugs. On the front of bioorthogonal conjugation, 2-FPBA/APBA has been found to conjugate with α-nucleophiles under physiologic conditions with rate constant ( k2) over 1000 M-1 s-1, which overcomes the slow kinetics problems and rekindles the interest of using the conjugation of α-nucleophiles for biological studies. With fast kinetics being a shared feature, this family of conjugation chemistries gives remarkably diverse product structures depending on the choice of nucleophile. Importantly, both dynamic and irreversible conjugations have been developed, which we believe will enable a wide array of applications in biological research. In this Account, we collectively examine this rapidly expanding family of conjugation reactions, seeking to elucidate the unifying principles that would guide further development of novel conjugation reactions, as well as their applications in biology.
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Affiliation(s)
- Samantha Cambray
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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35
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Akgun B, Hall DG. Boronsäuren als bioorthogonale Sonden für zentrenselektives Protein‐Labeling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712611] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
| | - Dennis G. Hall
- Department of Chemistry – CCIS 4-010University of Alberta Edmonton Alberta T6G 2G2 Kanada
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36
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Qin LH, Hu W, Long YQ. Bioorthogonal chemistry: Optimization and application updates during 2013–2017. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Larsen D, Kietrys AM, Clark SA, Park HS, Ekebergh A, Kool ET. Exceptionally rapid oxime and hydrazone formation promoted by catalytic amine buffers with low toxicity. Chem Sci 2018; 9:5252-5259. [PMID: 29997880 PMCID: PMC6001384 DOI: 10.1039/c8sc01082j] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
Hydrazone and oxime bond formation between α-nucleophiles (e.g. hydrazines, alkoxy-amines) and carbonyl compounds (aldehydes and ketones) is convenient and is widely applied in multiple fields of research. While the reactants are simple, a substantial drawback is the relatively slow reaction at neutral pH. Here we describe a novel molecular strategy for accelerating these reactions, using bifunctional buffer compounds that not only control pH but also catalyze the reaction. The buffers can be employed at pH 5-9 (5-50 mM) and accelerate reactions by several orders of magnitude, yielding second-order rate constants of >10 M-1 s-1. Effective bifunctional amines include 2-(aminomethyl)imidazoles and N,N-dimethylethylenediamine. Unlike previous diaminobenzene catalysts, the new buffer amines are found to have low toxicity to human cells, and can be used to promote reactions in cellular applications.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Anna M Kietrys
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Spencer A Clark
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Hyun Shin Park
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Andreas Ekebergh
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
| | - Eric T Kool
- Department of Chemistry , Stanford University , Stanford , CA 94305 , USA .
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38
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Abstract
Chemical tools are transforming our understanding of biomolecules and living systems. Included in this group are bioorthogonal reagents-functional groups that are inert to most biological species, but can be selectively ligated with complementary probes, even in live cells and whole organisms. Applications of these tools have revealed fundamental new insights into biomolecule structure and function-information often beyond the reach of genetic approaches. In many cases, the knowledge gained from bioorthogonal probes has enabled new questions to be asked and innovative research to be pursued. Thus, the continued development and application of these tools promises to both refine our view of biological systems and facilitate new discoveries. Despite decades of achievements in bioorthogonal chemistry, limitations remain. Several reagents are too large or insufficiently stable for use in cellular environments. Many bioorthogonal groups also cross-react with one another, restricting them to singular tasks. In this Account, we describe our work to address some of the voids in the bioorthogonal toolbox. Our efforts to date have focused on small reagents with a high degree of tunability: cyclopropenes, triazines, and cyclopropenones. These motifs react selectively with complementary reagents, and their unique features are enabling new pursuits in biology. The Account is organized by common themes that emerged in our development of novel bioorthogonal reagents and reactions. First, natural product structures can serve as valuable starting points for probe design. Cyclopropene, triazine, and cyclopropenone motifs are all found in natural products, suggesting that they would be metabolically stable and compatible with a variety of living systems. Second, fine-tuning bioorthogonal reagents is essential for their successful translation to biological systems. Different applications demand different types of probes; thus, generating a collection of tools that span a continuum of reactivities and stabilities remains an important goal. We have used both computational analyses and mechanistic studies to guide the optimization of various cyclopropene and triazine probes. Along the way, we identified reagents that are chemoselective but best suited for in vitro work. Others are selective and robust enough for use in living organisms. The last section of this Account highlights the need for the continued pursuit of new reagents and reactions. Challenges exist when bioorthogonal chemistries must be used in concert, given that many exploit similar mechanisms and cannot be used simultaneously. Such limitations have precluded certain multicomponent labeling studies and other biological applications. We have relied on mechanistic and computational insights to identify mutually orthogonal sets of reactions, in addition to exploring unique genres of reactivity. The continued development of mechanistically distinct, biocompatible reactions will further diversify the bioorthogonal reaction portfolio for examining biomolecules.
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Abstract
A [1]rotaxane with two threaded α-cyclodextrin (α-CD) wheels was synthesized in 92% yield using a one-pot process at room temperature that employed spontaneous α-CD threading onto a 12-carbon alkyl chain in water followed by an oxime condensation reaction that attached two boronic acid-containing stopper groups. Rapid pirouetting of the threaded α-CD wheels around the encapsulated dumbbell was switched "ON" or "OFF" by the presence of chemical additives that controlled boronate ester bond formation between the interlocked components.
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Affiliation(s)
- Qi-Wei Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Jaroslav Zajíček
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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40
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Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH. Sci Rep 2018; 8:2193. [PMID: 29391582 PMCID: PMC5794741 DOI: 10.1038/s41598-018-20735-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022] Open
Abstract
We have discovered a simple and versatile reaction condition for oxime mediated bioconjugation reaction that could be adapted for both aldehyde and keto substrates. We found that saline accelerated the oxime kinetics in a concentration-dependent manner under physiological conditions. The reaction mechanism is validated by computational studies, and the versatility of the reaction is demonstrated by cell-surface labeling experiments. Saline offers an efficient and non-toxic catalytic option for performing the bioorthogonal-coupling reaction of biomolecules at the physiological pH. This saline mediated bioconjugation reaction represents the most biofriendly, mild and versatile approach for conjugating sensitive biomolecules and does not require any extensive purification step.
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41
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Gillingham D. The role of boronic acids in accelerating condensation reactions of α-effect amines with carbonyls. Org Biomol Chem 2018; 14:7606-9. [PMID: 27424916 DOI: 10.1039/c6ob01193d] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A broad palette of bioconjugation reactions are available for chemical biologists, but an area that still requires investigation is high-rate constant reactions. These are indispensable in certain applications, particularly for in vivo labelling. Appropriately positioned boronic acids accelerate normally sluggish Schiff base condensations of α-effect nucleophiles by five orders of magnitude - providing a new entry to the rare set of reactions that have a rate constant above 100 M(-1) s(-1) under physiological conditions. I summarize here a number of recent reports, including work from my own group, and outline a mechanistic picture that explains the differing behaviour of seemingly similar substrate classes.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland.
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42
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Li K, Weidman C, Gao J. Dynamic Formation of Imidazolidino Boronate Enables Design of Cysteine-Responsive Peptides. Org Lett 2018; 20:20-23. [PMID: 29261321 PMCID: PMC6475808 DOI: 10.1021/acs.orglett.7b03116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe the dynamic and chemoselective conjugation between 2-formylphenylboronic acid and l-2,3-diaminopropionic acid yielding an imidazolidino boronate (IzB) complex. The IzB complex formation readily proceeds in biological milieu with little interference by common biomolecules except cysteine. We demonstrate the potential of this reversible conjugation for biological applications by creating "smart" peptides that specifically respond to cysteine in complex biological media. Specifically, the design and characterization of a fluorogenic sensor of cysteine is described.
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Affiliation(s)
- Kaicheng Li
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Chelsea Weidman
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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43
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Nisal R, P. Jose G, Shanbhag C, Kalia J. Rapid and reversible hydrazone bioconjugation in cells without the use of extraneous catalysts. Org Biomol Chem 2018; 16:4304-4310. [DOI: 10.1039/c8ob00946e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rapid, catalyst-free and reversible bioconjugation in mammalian cells.
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Affiliation(s)
- Rahul Nisal
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Gregor P. Jose
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Chitra Shanbhag
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
| | - Jeet Kalia
- Indian Institute of Science Education and Research (IISER) Pune
- Pune-411008
- India
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44
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Liew SK, Holownia A, Diaz DB, Cistrone PA, Dawson PE, Yudin AK. Borylated oximes: versatile building blocks for organic synthesis. Chem Commun (Camb) 2017; 53:11237-11240. [PMID: 28959806 PMCID: PMC6097236 DOI: 10.1039/c7cc06579e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we demonstrate the synthesis and functionalization of α-boryl aldoximes from α-boryl aldehydes, with no sign of C-to-N boryl migration. Selective modification of the oxime functionality enables access to a wide range of borylated compounds, such as borylated heterocycles and N-acetoxyamides. By reducing the α-boryl aldoximes, MIDA deprotection yields the corresponding β-boryl hydroxylamines. As part of this study, we also demonstrate the utility of the boryl aldoxime motif in peptide conjugation.
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Affiliation(s)
- Sean K Liew
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
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45
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Akgun B, Li C, Hao Y, Lambkin G, Derda R, Hall DG. Synergic “Click” Boronate/Thiosemicarbazone System for Fast and Irreversible Bioorthogonal Conjugation in Live Cells. J Am Chem Soc 2017; 139:14285-14291. [DOI: 10.1021/jacs.7b08693] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Burcin Akgun
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Caishun Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yubin Hao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gareth Lambkin
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Dennis G. Hall
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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46
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Gu H, Chio TI, Lei Z, Staples RJ, Hirschi JS, Bane S. Formation of hydrazones and stabilized boron-nitrogen heterocycles in aqueous solution from carbohydrazides and ortho-formylphenylboronic acids. Org Biomol Chem 2017; 15:7543-7548. [PMID: 28853481 PMCID: PMC6636819 DOI: 10.1039/c7ob01708a] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A recent addition to the suite of fast bioorthogonal reactions combines hydrazines and hydroxylamines with ortho-carbonyl substituted phenylboronic acids. Carbohydrazides are easily incorporated into biomolecules, making them appealing substrates in these reactions. Here we show that simple alkyl carbohydrazides form a single product with ortho-formylphenylboronic acid in an organic solvent and in the solid state. The solution structures of the products formed from the carbohydrazides in buffered aqueous solution, however, are markedly different from those identified in the organic solvent and solid state. The reactants form a mixture of hydrazone and heterocyclic products, the relative composition of which varies with pH. The observed reversibility of bioconjugates using carbohydrazide can thus be explained by the reversibility of the boron-nitrogen bond in the heterocycle. In contrast, the inclusion of an α-amine into the carbohydrazide substrate yields a single product in which both nitrogens are bonded to boron. These tricyclic structures are the same in organic solvent, solid state and aqueous solution from pH 4 to pH 9. Bioconjugates formed with α-amino carbohydrazides are stable to SDS-PAGE, while those formed with simple alkyl carbohydrazides are not. We propose that the inclusion of an intramolecular stabilizing ligand into a carbohydrazide substrate is a generally applicable principle that may be exploited to form boronic acid-based bioconjugates with a defined structure and resistance to hydrolysis.
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Affiliation(s)
- Han Gu
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA.
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47
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Hentzen NB, Smeenk LEJ, Witek J, Riniker S, Wennemers H. Cross-Linked Collagen Triple Helices by Oxime Ligation. J Am Chem Soc 2017; 139:12815-12820. [PMID: 28872857 DOI: 10.1021/jacs.7b07498] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covalent cross-links are crucial for the folding and stability of triple-helical collagen, the most abundant protein in nature. Cross-linking is also an attractive strategy for the development of synthetic collagen-based biocompatible materials. Nature uses interchain disulfide bridges to stabilize collagen trimers. However, their implementation into synthetic collagen is difficult and requires the replacement of the canonical amino acids (4R)-hydroxyproline and proline by cysteine or homocysteine, which reduces the preorganization and thereby stability of collagen triple helices. We therefore explored alternative covalent cross-links that allow for connecting triple-helical collagen via proline residues. Here, we present collagen model peptides that are cross-linked by oxime bonds between 4-aminooxyproline (Aop) and 4-oxoacetamidoproline placed in coplanar Xaa and Yaa positions of neighboring strands. The covalently connected strands folded into hyperstable collagen triple helices (Tm ≈ 80 °C). The design of the cross-links was guided by an analysis of the conformational properties of Aop, studies on the stability and functionalization of Aop-containing collagen triple helices, and molecular dynamics simulations. The studies also show that the aminooxy group exerts a stereoelectronic effect comparable to fluorine and introduce oxime ligation as a tool for the functionalization of synthetic collagen.
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Affiliation(s)
- Nina B Hentzen
- Laboratorium für Organische Chemie, ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Linde E J Smeenk
- Laboratorium für Organische Chemie, ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Jagna Witek
- Laboratorium für Physikalische Chemie, ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie, ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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48
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Abstract
The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.
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Affiliation(s)
- Dominik K Kölmel
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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49
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Liu X, Li Z, Xu H, Zhan Y, Ma P, Chen H, Jiang B. Tris(2-carboxyethyl)phosphine promotes hydrolysis of iminoboronates. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.06.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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50
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Li BJ, Simard RD, Beauchemin AM. o-Phthalaldehyde catalyzed hydrolysis of organophosphinic amides and other P([double bond, length as m-dash]O)-NH containing compounds. Chem Commun (Camb) 2017; 53:8667-8670. [PMID: 28726879 DOI: 10.1039/c7cc04950a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over 50 years ago, Jencks and Gilchrist showed that formaldehyde catalyses the hydrolysis of phosphoramidate through electrophilic activation, induced by covalent attachment to its nitrogen atom. Given our interest in the use of aldehydes as catalysts, this work was revisited to identify a superior catalyst, o-phthalaldehyde, which facilitates hydrolyses of various organophosphorus compounds bearing P([double bond, length as m-dash]O)-NH subunits under mild conditions. Interestingly, chemoselective hydrolysis of the P([double bond, length as m-dash]O)-N bonds could be accomplished in the presence of P([double bond, length as m-dash]O)-OR bonds.
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Affiliation(s)
- Bin-Jie Li
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada.
| | - Ryan D Simard
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada.
| | - André M Beauchemin
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada.
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