1
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Vidyakina AA, Silonov SA, Govdi AI, Ivanov AY, Podolskaya EP, Balova IA, Bräse S, Danilkina NA. Key role of cycloalkyne nature in alkyne-dye reagents for enhanced specificity of intracellular imaging by bioorthogonal bioconjugation. Org Biomol Chem 2024. [PMID: 38973457 DOI: 10.1039/d4ob01032a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Conjugates of benzothiophene-fused azacyclononyne BT9N-NH2 with fluorescent dyes were developed to visualise azidoglycans intracellularly. The significance of the cycloalkyne core was demonstrated by comparing new reagents with DBCO- and BCN-dye conjugates. To reduce non-specificity during intracellular bioconjugation using SPAAC, less reactive BT9N-dye reagents are preferred over highly reactive DBCO- and BCN-dye conjugates.
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Affiliation(s)
- Alexandra A Vidyakina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Sergey A Silonov
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064, Russia
| | - Anastasia I Govdi
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Alexander Yu Ivanov
- Center for Magnetic Resonance, Research Park, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia
| | | | - Irina A Balova
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany.
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Natalia A Danilkina
- Institute of Chemistry, Saint Petersburg State University (SPbU), Saint Petersburg, 199034, Russia.
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2
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Guo M, Lei Y, Zhao K, Guo L, Dang B. A single backbone amide modification method to achieve single site-specific chemical protein conjugation. Methods Enzymol 2024; 698:57-88. [PMID: 38886040 DOI: 10.1016/bs.mie.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Efficient and precise chemical protein modification methods are highly sought after in biotechnology. However, chemically distinguishing a single site within a large protein is challenging. This study introduces a Copper Assisted Sequence-specific Conjugation Tag (CAST) method, enabling rapid (second order rate 8.1 M-1s-1) and site-specific chemical modification of the protein backbone with pinpoint accuracy. The versatility of this method is demonstrated through the preparation of antibody-drug conjugates, showcasing high plasma stability and potent efficacy in both in vitro and in vivo settings. Thus, CAST emerges as an efficient and quantitative approach for attaching payloads to large, native proteins.
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Affiliation(s)
- Mengzhun Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Yingjie Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Kai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Liang Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China
| | - Bobo Dang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, P.R. China; Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, P.R. China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, P.R. China.
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3
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Giltrap A, Yuan Y, Davis BG. Late-Stage Functionalization of Living Organisms: Rethinking Selectivity in Biology. Chem Rev 2024; 124:889-928. [PMID: 38231473 PMCID: PMC10870719 DOI: 10.1021/acs.chemrev.3c00579] [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] [Received: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/18/2024]
Abstract
With unlimited selectivity, full post-translational chemical control of biology would circumvent the dogma of genetic control. The resulting direct manipulation of organisms would enable atomic-level precision in "editing" of function. We argue that a key aspect that is still missing in our ability to do this (at least with a high degree of control) is the selectivity of a given chemical reaction in a living organism. In this Review, we systematize existing illustrative examples of chemical selectivity, as well as identify needed chemical selectivities set in a hierarchy of anatomical complexity: organismo- (selectivity for a given organism over another), tissuo- (selectivity for a given tissue type in a living organism), cellulo- (selectivity for a given cell type in an organism or tissue), and organelloselectivity (selectivity for a given organelle or discrete body within a cell). Finally, we analyze more traditional concepts such as regio-, chemo-, and stereoselective reactions where additionally appropriate. This survey of late-stage biomolecule methods emphasizes, where possible, functional consequences (i.e., biological function). In this way, we explore a concept of late-stage functionalization of living organisms (where "late" is taken to mean at a given state of an organism in time) in which programmed and selective chemical reactions take place in life. By building on precisely analyzed notions (e.g., mechanism and selectivity) we believe that the logic of chemical methodology might ultimately be applied to increasingly complex molecular constructs in biology. This could allow principles developed at the simple, small-molecule level to progress hierarchically even to manipulation of physiology.
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Affiliation(s)
- Andrew
M. Giltrap
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Yizhi Yuan
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
| | - Benjamin G. Davis
- The
Rosalind Franklin Institute, Oxfordshire OX11 0FA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, U.K.
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4
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Sydenham JD, Seki H, Krajcovicova S, Zeng L, Schober T, Deingruber T, Spring DR. Site-selective peptide functionalisation mediated via vinyl-triazine linchpins. Chem Commun (Camb) 2024; 60:706-709. [PMID: 38108130 DOI: 10.1039/d3cc05213c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Herein we introduce 3-vinyl-1,2,4-triazines derivatives as dual-reactive linkers that exhibit selectivity towards cysteine and specific strained alkynes, enabling conjugate addition and inverse electron-demand Diels-Alder (IEDDA) reactions. This approach facilitates site-selective bioconjugation of biologically relevant peptides, followed by rapid and highly selective reactions with bicyclononyne (BCN) reagents.
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Affiliation(s)
- Jack D Sydenham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Hikaru Seki
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Sona Krajcovicova
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
- Department of Organic Chemistry, Palacky University in Olomouc, Tr. 17. Listopadu 12, Olomouc, Czech Republic
| | - Linwei Zeng
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Tim Schober
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Tomas Deingruber
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
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5
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Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
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Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
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6
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Peschke F, Taladriz‐Sender A, Andrews MJ, Watson AJB, Burley GA. Glutathione Mediates Control of Dual Differential Bio-orthogonal Labelling of Biomolecules. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202313063. [PMID: 38515866 PMCID: PMC10953330 DOI: 10.1002/ange.202313063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Indexed: 03/23/2024]
Abstract
Traditional approaches to bio-orthogonal reaction discovery have focused on developing reagent pairs that react with each other faster than they are metabolically degraded. Glutathione (GSH) is typically responsible for the deactivation of most bio-orthogonal reagents. Here we demonstrate that GSH promotes a Cu-catalysed (3+2) cycloaddition reaction between an ynamine and an azide. We show that GSH acts as a redox modulator to control the Cu oxidation state in these cycloadditions. Rate enhancement of this reaction is specific for ynamine substrates and is tuneable by the Cu:GSH ratio. This unique GSH-mediated reactivity gradient is then utilised in the dual sequential bio-orthogonal labelling of peptides and oligonucleotides via two distinct chemoselective (3+2) cycloadditions.
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Affiliation(s)
- Frederik Peschke
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
| | - Andrea Taladriz‐Sender
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
| | - Matthew J. Andrews
- EaStCHEMSchool of ChemistryUniversity of Saint AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Allan J. B. Watson
- EaStCHEMSchool of ChemistryUniversity of Saint AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Glenn A. Burley
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
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7
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Peschke F, Taladriz‐Sender A, Andrews MJ, Watson AJB, Burley GA. Glutathione Mediates Control of Dual Differential Bio-orthogonal Labelling of Biomolecules. Angew Chem Int Ed Engl 2023; 62:e202313063. [PMID: 37906440 PMCID: PMC10952886 DOI: 10.1002/anie.202313063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Traditional approaches to bio-orthogonal reaction discovery have focused on developing reagent pairs that react with each other faster than they are metabolically degraded. Glutathione (GSH) is typically responsible for the deactivation of most bio-orthogonal reagents. Here we demonstrate that GSH promotes a Cu-catalysed (3+2) cycloaddition reaction between an ynamine and an azide. We show that GSH acts as a redox modulator to control the Cu oxidation state in these cycloadditions. Rate enhancement of this reaction is specific for ynamine substrates and is tuneable by the Cu:GSH ratio. This unique GSH-mediated reactivity gradient is then utilised in the dual sequential bio-orthogonal labelling of peptides and oligonucleotides via two distinct chemoselective (3+2) cycloadditions.
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Affiliation(s)
- Frederik Peschke
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
| | - Andrea Taladriz‐Sender
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
| | - Matthew J. Andrews
- EaStCHEMSchool of ChemistryUniversity of Saint AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Allan J. B. Watson
- EaStCHEMSchool of ChemistryUniversity of Saint AndrewsNorth HaughSt AndrewsFifeKY16 9STUK
| | - Glenn A. Burley
- Department of Pure & Applied Chemistry & the Strathclyde Centre for Molecular BioscienceUniversity of Strathclyde295 Cathedral StreetGlasgowG1 1XLUK
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8
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Guo M, Zhao K, Guo L, Zhou R, He Q, Lu K, Li T, Liu D, Chen J, Tang J, Fu X, Zhou J, Zheng B, Mann SI, Zhang Y, Huang J, Yang B, Zhou T, Lei Y, Dang B. Copper assisted sequence-specific chemical protein conjugation at a single backbone amide. Nat Commun 2023; 14:8063. [PMID: 38052794 DOI: 10.1038/s41467-023-43753-7] [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: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Direct, site-specific methods of protein functionalization are highly desirable for biotechnology. However, such methods are challenging due to the difficulty of chemically differentiating a single site within a large protein. Herein, we propose "metal binding targeting" strategy and develop a Copper Assisted Sequence-specific conjugation Tag (CAST) method to achieve rapid (second order rate 8.1 M-1 s-1), site-specific protein backbone chemical modification with pinpoint accuracy. We demonstrate the versatility of CAST conjugation by preparing various on-demand modified recombinant proteins, including a homogeneous antibody-drug conjugate with high plasma stability and potent efficacy in vitro and in vivo. Thus, CAST provides an efficient and quantitative method to site-specifically attach payloads on large, native proteins.
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Affiliation(s)
- Mengzhun Guo
- Fudan University, Shanghai, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Kai Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Liang Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rui Zhou
- Department of Nuclear Medicine and Positron Emission Tomography Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Qiuju He
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Kuan Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Tian Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Dandan Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinfeng Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jing Tang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xin Fu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jinyun Zhou
- Department of Nuclear Medicine and Positron Emission Tomography Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Bei Zheng
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Samuel I Mann
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Yongdeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jing Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Yingjie Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Bobo Dang
- Fudan University, Shanghai, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future and Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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9
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Bleton O, Beaucage N, Guerrero-Morales J, Collins SK. Photocatalytic Thiol-Yne Reactions of Alkynyl Sulfides. J Org Chem 2023. [PMID: 38019972 DOI: 10.1021/acs.joc.3c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Thiol-yne reactions typically employ thiols and terminal alkynes as the reaction partners. The thiol-yne reaction of alkynyl sulfides and thiols is possible when employing a nonmetal photocatalyst eosin Y, green LED irradiation, under an air atmosphere. Alkynyl sulfides were transformed in good overall yields (58-90% total yields, 11 examples) favoring the cis isomer. No addition to the α-position of the alkynyl sulfide is observed, and regioselectivity is believed to be controlled through the stabilization of radical intermediates by the adjacent sulfur atom. Furthermore, control experiments with "all-carbon" internal alkynes demonstrate that alkynyl sulfides possess improved reactivity and regioselectivity profiles during thiol-yne processes.
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Affiliation(s)
- Oliver Bleton
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
| | - Noémie Beaucage
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
| | - Javier Guerrero-Morales
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
| | - Shawn K Collins
- Département de Chimie, Centre for Green Chemistry and Catalysis, Université de Montréal, Complexe des Sciences, 1375 Avenue Thérèse-Lavoie-Roux, Montréal H2 V 0B3, Québec, Canada
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10
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Sasso J, Tenchov R, Bird R, Iyer KA, Ralhan K, Rodriguez Y, Zhou QA. The Evolving Landscape of Antibody-Drug Conjugates: In Depth Analysis of Recent Research Progress. Bioconjug Chem 2023; 34:1951-2000. [PMID: 37821099 PMCID: PMC10655051 DOI: 10.1021/acs.bioconjchem.3c00374] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Antibody-drug conjugates (ADCs) are targeted immunoconjugate constructs that integrate the potency of cytotoxic drugs with the selectivity of monoclonal antibodies, minimizing damage to healthy cells and reducing systemic toxicity. Their design allows for higher doses of the cytotoxic drug to be administered, potentially increasing efficacy. They are currently among the most promising drug classes in oncology, with efforts to expand their application for nononcological indications and in combination therapies. Here we provide a detailed overview of the recent advances in ADC research and consider future directions and challenges in promoting this promising platform to widespread therapeutic use. We examine data from the CAS Content Collection, the largest human-curated collection of published scientific information, and analyze the publication landscape of recent research to reveal the exploration trends in published documents and to provide insights into the scientific advances in the area. We also discuss the evolution of the key concepts in the field, the major technologies, and their development pipelines with company research focuses, disease targets, development stages, and publication and investment trends. A comprehensive concept map has been created based on the documents in the CAS Content Collection. We hope that this report can serve as a useful resource for understanding the current state of knowledge in the field of ADCs and the remaining challenges to fulfill their potential.
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Affiliation(s)
- Janet
M. Sasso
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
| | - Rumiana Tenchov
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
| | - Robert Bird
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
| | | | | | - Yacidzohara Rodriguez
- CAS,
A Division of the American Chemical Society, Columbus, Ohio 43210, United States
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11
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Tavakoli S, Evans A, Oommen OP, Creemers L, Nandi JB, Hilborn J, Varghese OP. Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry. Mater Today Bio 2023; 22:100768. [PMID: 37600348 PMCID: PMC10432810 DOI: 10.1016/j.mtbio.2023.100768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.
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Affiliation(s)
- Shima Tavakoli
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Austin Evans
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Oommen P. Oommen
- Bioengineering and Nanomedicine Group, Faculty of Medicine and Health Technologies, Tampere University, 33720, Tampere, Finland
| | - Laura Creemers
- Department of Orthopedics, University Medical Center Utrecht, 3584, CX, Utrecht, the Netherlands
| | - Jharna Barman Nandi
- Department of Chemistry, Sarojini Naidu College for Women, 30 Jessore Road, Kolkata, 700028, India
| | - Jöns Hilborn
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
| | - Oommen P. Varghese
- Macromolecular Chemistry Division, Department of Chemistry–Ångström Laboratory, Uppsala University, 751 21, Uppsala, Sweden
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12
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Stone DJ, Macias-Contreras M, Crist SM, Bucag CFT, Seo G, Zhu L. SNAP-tagging live cells via chelation-assisted copper-catalyzed azide-alkyne cycloaddition. Org Biomol Chem 2023; 21:7419-7436. [PMID: 37665276 DOI: 10.1039/d3ob01003a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
SNAP-tag is a single-turnover enzyme that has become a powerful tool, hence a popular choice, of targeted cellular protein labeling. Three SNAP-tag substrates that carry the copper-chelating 2-picolyl azide moiety are prepared, one of which has an unconventional 5-pyridylmethyl-substituted guanine structure, rather than the usual benzylguanine that is optimized to be accepted by SNAP-tag. All three substrates are effective in transferring a 2-picolyl azide moiety to SNAP-tag in live cells under conventional labeling conditions (30-minute incubation of cells with labeling reagents at 37 °C under 5% CO2). Live cells that are decorated with chelating azido groups on the extracellular side of membranes undergo copper-catalyzed azide-alkyne cycloaddition (CuAAC) with an ethynyl-functionalized fluorophore to accomplish membrane protein labeling by a fluorescent dye. The chelation-assisted CuAAC labeling step is rapid (<1 minute) with a relatively low dose of the copper catalyst (20 μM), and consequently exerts no ill effect on the labeled cells. A SNAP-tag substrate that carries a non-chelating azide moiety, on the other hand, fails to produce satisfactory labeling under the same constraints. The rapid, live cell-compatible SNAP-tag/chelation-assisted CuAAC two-step method expands the utility of SNAP-tag in protein labeling applications.
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Affiliation(s)
- Daniel J Stone
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Miguel Macias-Contreras
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Shaun M Crist
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Christelle F T Bucag
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
| | - Gwimoon Seo
- Institute of Molecular Biophysics, Florida State University, 91 Chieftan Way, Tallahassee, FL 32306-4380, USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, USA.
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13
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Obeng EM, Steer DL, Fulcher A, Wagstaff KM. Steric-Deficient Oligoglycine Surrogates Facilitate Multivalent and Bifunctional Nanobody Synthesis via Combined Sortase A Transpeptidation and Click Chemistry. Bioconjug Chem 2023; 34:1667-1678. [PMID: 37534819 DOI: 10.1021/acs.bioconjchem.3c00319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Conferring multifunctional properties to proteins via enzymatic approaches has greatly facilitated recent progress in protein nanotechnology. In this regard, sortase (Srt) A transpeptidation has facilitated many of these developments due to its exceptional specificity, mild reaction conditions, and complementation with other bioorthogonal techniques, such as click chemistry. In most of these developments, Srt A is used to seamlessly tether oligoglycine-containing molecules to a protein of interest that is equipped with the enzyme's recognition sequence, LPXTG. However, the dependence on oligoglycine attacking nucleophiles and the associated cost of certain derivatives (e.g., cyclooctyne) limit the utility of this approach to lab-scale applications only. Thus, the quest to identify appropriate alternatives and understand their effectiveness remains an important area of research. This study identifies that steric and nucleophilicity-associated effects influence Srt A transpeptidation when two oligoglycine surrogates were examined. The approach was further used in complementation with click chemistry to synthesize bivalent and bifunctional nanobody conjugates for application in epithelial growth factor receptor targeting. The overall technique and tools developed here may facilitate the advancement of future nanotechnologies.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - David L Steer
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, Victoria, Australia
| | - Alex Fulcher
- Monash Micro Imaging, Monash University, Clayton 3800, Victoria, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
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14
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Bugatti K. A Brief Guide to Preparing a Peptide-Drug Conjugate. Chembiochem 2023; 24:e202300254. [PMID: 37288718 DOI: 10.1002/cbic.202300254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/09/2023]
Abstract
Peptide-drug conjugates (PDCs) have recently emerged as interesting hybrid constructs not only for targeted therapy, but also for the early diagnosis of different pathologies. In most cases, the crucial step in the PDC synthesis is the final conjugation step, where a specific drug is bound to a particular peptide-/peptidomimetic-targeting unit. Thus, this concept paper aims to give a short guide to determining the finest conjugation reaction, by considering in particular the reaction conditions, the stability of the linker and the major pros and cons of each reaction. Based on the recent PDCs reported in literature, the most common and efficient conjugation methods will be systematically presented and compared, generating a short guide to consult while planning the synthesis of a novel peptide-drug conjugate.
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Affiliation(s)
- Kelly Bugatti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy
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15
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Mata JM, van der Nol E, Pomplun SJ. Advances in Ultrahigh Throughput Hit Discovery with Tandem Mass Spectrometry Encoded Libraries. J Am Chem Soc 2023; 145:19129-19139. [PMID: 37556835 PMCID: PMC10472510 DOI: 10.1021/jacs.3c04899] [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: 05/11/2023] [Indexed: 08/11/2023]
Abstract
Discovering new bioactive molecules is crucial for drug development. Finding a hit compound for a new drug target usually requires screening of millions of molecules. Affinity selection based technologies have revolutionized early hit discovery by enabling the rapid screening of libraries with millions or billions of compounds in short timeframes. In this Perspective, we describe recent technology breakthroughs that enable the screening of ultralarge synthetic peptidomimetic libraries with a barcode-free tandem mass spectrometry decoding strategy. A combination of combinatorial synthesis, affinity selection, automated de novo peptide sequencing algorithms, and advances in mass spectrometry instrumentation now enables hit discovery from synthetic libraries with over 100 million members. We provide a perspective on this powerful technology and showcase success stories featuring the discovery of high affinity binders for a number of drug targets including proteins, nucleic acids, and specific cell types. Further, we show the usage of the technology to discover synthetic peptidomimetics with specific functions and reactivity. We predict that affinity selection coupled with tandem mass spectrometry and automated de novo decoding will rapidly evolve further and become a broadly used drug discovery technology.
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16
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Vasić K, Knez Ž, Leitgeb M. Transglutaminase in Foods and Biotechnology. Int J Mol Sci 2023; 24:12402. [PMID: 37569776 PMCID: PMC10419021 DOI: 10.3390/ijms241512402] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Stabilization and reusability of enzyme transglutaminase (TGM) are important goals for the enzymatic process since immobilizing TGM plays an important role in different technologies and industries. TGM can be used in many applications. In the food industry, it plays a role as a protein-modifying enzyme, while, in biotechnology and pharmaceutical applications, it is used in mediated bioconjugation due to its extraordinary crosslinking ability. TGMs (EC 2.3.2.13) are enzymes that catalyze the formation of a covalent bond between a free amino group of protein-bound or peptide-bound lysine, which acts as an acyl acceptor, and the γ-carboxamide group of protein-bound or peptide-bound glutamine, which acts as an acyl donor. This results in the modification of proteins through either intramolecular or intermolecular crosslinking, which improves the use of the respective proteins significantly.
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Affiliation(s)
- Katja Vasić
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia; (K.V.); (Ž.K.)
| | - Željko Knez
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia; (K.V.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, SI-2000 Maribor, Slovenia
| | - Maja Leitgeb
- Laboratory for Separation Processes and Product Design, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia; (K.V.); (Ž.K.)
- Faculty of Medicine, University of Maribor, Taborska Ulica 8, SI-2000 Maribor, Slovenia
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17
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O WY, Cui JF, Yu Q, Kung KKY, Chung SF, Leung YC, Wong MK. Isoindolium-Based Allenes: Reactivity Studies and Applications in Fluorescence Temperature Sensing and Cysteine Bioconjugation. Angew Chem Int Ed Engl 2023; 62:e202218038. [PMID: 36670048 DOI: 10.1002/anie.202218038] [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: 12/07/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The reaction of a series of electron-deficient isoindolium-based allenes with sulfhydryl compounds has been studied, leading to the formation of isoindolium-based vinyl sulfides. The vinyl sulfides generated could be readily converted into the corresponding indanones and amines upon heating at 30-70 °C with good yields up to 61 %. The thermal cleavage reaction of vinyl sulfides was further studied for developing temperature-sensitive systems. Notably, a novel FRET-based fluorescent temperature sensor was designed and synthesized for temperature sensing at 50 °C, giving a 6.5-fold blue fluorescence enhancement. Moreover, chemoselective bioconjugation of cysteine-containing peptides with the isoindolium-based allenes for the construction of multifunctional peptide bioconjugates was investigated. Thermal cleavage of isoindoliums on the modified peptides at 35-70 °C gave indanone bioconjugates with up to >99 % conversion. These results indicated the biocompatibility of this novel temperature-sensitive reaction.
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Affiliation(s)
- Wa-Yi O
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jian-Fang Cui
- Department of Chemistry, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, 518055, China
| | - Qiong Yu
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Karen Ka-Yan Kung
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
| | - Sai-Fung Chung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Yun-Chung Leung
- Henry Cheng Research Laboratory for Drug Development, Lo Ka Chung Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Man-Kin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food, Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China.,The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, 518057, China
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18
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Warashina S, Sato H, Zouda M, Takahashi M, Wada Y, Passioura T, Suga H, Watanabe Y, Matsumoto K, Mukai H. Two-Chain Mature Hepatocyte Growth Factor-Specific Positron Emission Tomography Imaging in Tumors Using 64Cu-Labeled HiP-8, a Nonstandard Macrocyclic Peptide Probe. Mol Pharm 2023; 20:2029-2038. [PMID: 36862642 DOI: 10.1021/acs.molpharmaceut.2c01020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Two-chain hepatocyte growth factor (tcHGF), the mature form of HGF, is associated with malignancy and anticancer drug resistance; therefore, its quantification is an important indicator for cancer diagnosis. In tumors, activated tcHGF hardly discharges into the systemic circulation, indicating that tcHGF is an excellent target for molecular imaging using positron emission tomography (PET). We recently discovered HGF-inhibitory peptide-8 (HiP-8) that binds specifically to human tcHGF with nanomolar affinity. The purpose of this study was to investigate the usefulness of HiP-8-based PET probes in human HGF knock-in humanized mice. 64Cu-labeled HiP-8 molecules were synthesized using a cross-bridged cyclam chelator, CB-TE1K1P. Radio-high-performance liquid chromatography-based metabolic stability analyses showed that more than 90% of the probes existed in intact form in blood at least for 15 min. In PET studies, significantly selective visualization of hHGF-overexpressing tumors versus hHGF-negative tumors was observed in double-tumor-bearing mice. The accumulation of labeled HiP-8 into the hHGF-overexpressing tumors was significantly reduced by competitive inhibition. In addition, the radioactivity and distribution of phosphorylated MET/HGF receptor were colocalized in tissues. These results demonstrate that the 64Cu-labeled HiP-8 probes are suitable for tcHGF imaging in vivo, and secretory proteins like tcHGF can be a target for PET imaging.
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Affiliation(s)
- Shota Warashina
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Hiroki Sato
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Maki Zouda
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Maiko Takahashi
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Wada
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kunio Matsumoto
- Division of Tumor Dynamics and Regulation, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.,WPI-Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidefumi Mukai
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Department of Pharmaceutical Informatics, Graduate School of Biomedical Science, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
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19
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Tao W, He W, Feng X, Liu G, Shi Q, Tan J, Hu J, Yang S, Liu G, Yang R. Cationic Single-Unit Monomer Insertion (cSUMI): From Discrete Oligomers to the α-/ω-End and In-Chain Sequence-Regulated Polymers. J Am Chem Soc 2023; 145:3636-3646. [PMID: 36724078 DOI: 10.1021/jacs.2c12873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Single-unit monomer insertion (SUMI) has become an important strategy for the synthesis of sequence-controlled vinyl polymers due to its strong versatility and high efficiency. However, all reported SUMI processes are based on a free-radical mechanism, resulting in a limited number of monomer types being applicable to SUMI or a limited number of sequences of structural units that SUMI can synthesize. Herein, we developed a novel SUMI based on a cationic mechanism (cSUMI), which operates through a degenerative (similar to radical SUMI) but cationic chain transfer process. By optimizing the chain transfer agent (CTA) and monomer pairs, a high-efficiency cSUMI was achieved for vinyl ether and styrene monomers. Based on this reaction, a range of discrete oligomers containing vinyl ether and styrene moieties, and even α-/ω-end and in-chain sequence-regulated polymers were synthesized, most of which cannot be achieved by radical SUMI. In addition, we explored the application of these sequence-regulated polymers in the preparation of miktoarm star polymers, delivery of photosensitizers, and solubilization of fluorescence probes. The development of SUMI with a new mechanism will certainly broaden the scope of structures and sequences in precise vinyl-based polymers.
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Affiliation(s)
- Wei Tao
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.,Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei He
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Xuepu Feng
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Guoqin Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qiangqiang Shi
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiajia Tan
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinming Hu
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Sheng Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
| | - Guhuan Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China.,Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, China
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20
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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21
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Jensen KJ, Thygesen MB, Sørensen KK, Wu S, Treiberg T, Schoffelen S. Selective Acylation of Proteins at Gly and Lys in His Tags. Chembiochem 2022; 23:e202200359. [PMID: 35984670 DOI: 10.1002/cbic.202200359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/19/2022] [Indexed: 01/25/2023]
Abstract
The chemical modification of proteins is of great importance in chemical biology, biotechnology, and for the production of modified biopharmaceuticals, as it enables introduction of fluorophores, biotin, half-life extending moieties, and more. We have developed two methods that use poly-His sequences to direct the highly selective acylation of proteins, either at the N-terminus or at a specific Lys residue. For the former, we used an N-terminal Gly-His6 segment (Gly-His tag) that directed acylation of the N-terminal Nα -amine with 4-methoxyphenyl esters, resulting in stable conjugates. Next, we developed the peptide sequences Hisn -Lys-Hism (Lys-His tags) that direct the acylation of the designated Lys Nϵ -amine under mild conditions and with high selectivity over native Lys residues. Both the Gly-His and Lys-His tags maintain the capacity for immobilized metal ion affinity chromatography. We have demonstrated the robustness of these methods by attaching different moieties such as azides, fluorophores, and biotin to different proteins, including antibodies.
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Affiliation(s)
- Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Tuule Treiberg
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Sanne Schoffelen
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
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22
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Becker T, Wiest A, Telek A, Bejko D, Hoffmann-Röder A, Kielkowski P. Transforming Chemical Proteomics Enrichment into a High-Throughput Method Using an SP2E Workflow. JACS AU 2022; 2:1712-1723. [PMID: 35911458 PMCID: PMC9326820 DOI: 10.1021/jacsau.2c00284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Protein post-translational modifications (PTMs) play a critical role in the regulation of protein catalytic activity, localization, and protein-protein interactions. Attachment of PTMs onto proteins significantly diversifies their structure and function, resulting in proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease-specific, is still a highly challenging task. Substoichiometric amounts and modifications of low abundant proteins necessitate the purification or enrichment of the modified proteins. Although the introduction of mass spectrometry-based chemical proteomic strategies has enabled the screening of protein PTMs with increased throughput, sample preparation remains highly time-consuming and tedious. Here, we report an optimized workflow for the enrichment of PTM proteins in a 96-well plate format, which could be extended to robotic automation. This platform allows us to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult-to-culture cell lines in a high-throughput manner. The presented SP2E protocol is robust and time- and cost-effective, as well as suitable for large-scale screening of proteoforms. The application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration, and cancer. This may contribute to an overall acceleration of the recently launched Human Proteoform Project.
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Affiliation(s)
- Tobias Becker
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - Andreas Wiest
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - András Telek
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | - Daniel Bejko
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
| | | | - Pavel Kielkowski
- Institute
for Chemical Epigenetics Munich, LMU Munich, 81375 Munich, Germany
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23
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Kofoed C, Wu S, Sørensen KK, Treiberg T, Arnsdorf J, Bjørn SP, Jensen TL, Voldborg BG, Thygesen MB, Jensen KJ, Schoffelen S. Highly Selective Lysine Acylation in Proteins Using a Lys-His Tag Sequence. Chemistry 2022; 28:e202200147. [PMID: 35099088 DOI: 10.1002/chem.202200147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Indexed: 11/07/2022]
Abstract
Chemical modification of proteins has numerous applications, but it has been challenging to achieve the required high degree of selectivity on lysine amino groups. Recently, we described the highly selective acylation of proteins with an N-terminal Gly-His6 segment. This tag promoted acylation of the N-terminal Nα -amine resulting in stable conjugates. Herein, we report the peptide sequences Hisn -Lys-Hism , which we term Lys-His tags. In combination with simple acylating agents, they facilitate the acylation of the designated Lys Nϵ -amine under mild conditions and with high selectivity over native Lys residues. We show that the Lys-His tags, which are 7 to 10 amino acids in length and still act as conventional His tags, can be inserted in proteins at the C-terminus or in loops, thus providing high flexibility regarding the site of modification. Finally, the selective and efficient acylation of the therapeutic antibody Rituximab, pure or mixed with other proteins, demonstrates the scope of the Lys-His tag acylation method.
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Affiliation(s)
- Christian Kofoed
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Present address: Frick Chemistry Laboratories, Princeton University, 08544, New Jersey, USA
| | - Shunliang Wu
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Tuule Treiberg
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Johnny Arnsdorf
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Sara P Bjørn
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Tanja L Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Bjørn G Voldborg
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Mikkel B Thygesen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Sanne Schoffelen
- National Biologics Facility, Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
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24
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Obeng EM, Dzuvor CKO, Danquah MK. Anti-SARS-CoV-1 and -2 nanobody engineering towards avidity-inspired therapeutics. NANO TODAY 2022; 42:101350. [PMID: 34840592 PMCID: PMC8608585 DOI: 10.1016/j.nantod.2021.101350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 05/15/2023]
Abstract
In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and -2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.
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Affiliation(s)
- Eugene M Obeng
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, United States
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25
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Wang C, Zhao Y, Zhao J. Recent Advances in Chemical Protein Modification via Cysteine. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202203008] [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]
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26
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Sahu T, Kumar M, T. K. S, Joshi M, Mishra RK, Rai V. Residue-specific N-terminal glycine to aldehyde transformation renders analytically pure single-site labeled proteins. Chem Commun (Camb) 2022; 58:12451-12454. [DOI: 10.1039/d2cc04196k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we demonstrate the residue-specific transformation of N-Gly into N-Gly-glyoxamide. The aldehyde introduction opens the residue-specific synthetic flexibility for the N-Gly proteome.
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Affiliation(s)
- Tularam Sahu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Sajeev T. K.
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, MP 462 066, India
| | - Manas Joshi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
| | - Ram Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, MP 462 066, India
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, MP 462 066, India
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27
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Shen MH, Wang YJ, Wang Y, Zhou Y, Gu J, Liu XQ, Guo J, Ouyang M, Deng L, Xu HD. α-Vinyl azide–cysteine click coupling reaction enabled bioorthogonal peptide/protein modification. Org Chem Front 2022. [DOI: 10.1039/d2qo00736c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Alkyl and α-aryl vinyl azides were found to be able to couple with cysteine-derived alkyl thiols chemoselectively under mild conditions, providing the corresponding β-ketosulfides with simultaneous extrusion of N2 and ammonia.
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Affiliation(s)
- Mei-Hua Shen
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yu-Jiao Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Yong Wang
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Ying Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jie Gu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Xiao-Qian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Jia Guo
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Mingxing Ouyang
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Linhong Deng
- Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province, 213164, China
| | - Hua-Dong Xu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu Province, 213164, China
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28
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Zhang X, Ou C, Liu H, Prabhu SK, Li C, Yang Q, Wang LX. General and Robust Chemoenzymatic Method for Glycan-Mediated Site-Specific Labeling and Conjugation of Antibodies: Facile Synthesis of Homogeneous Antibody-Drug Conjugates. ACS Chem Biol 2021; 16:2502-2514. [PMID: 34569782 DOI: 10.1021/acschembio.1c00597] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Site-specific labeling and conjugation of antibodies are highly desirable for fundamental research and for developing more efficient diagnostic and therapeutic methods. We report here a general and robust chemoenzymatic method that permits a one-pot site-specific functionalization of antibodies. A series of selectively modified disaccharide oxazoline derivatives were designed, synthesized, and evaluated as donor substrates of different endoglycosidases for antibody Fc glycan remodeling. We found that among several endoglycosidases tested, wild-type endoglycosidase from Streptococcus pyogenes of serotype M49 (Endo-S2) exhibited remarkable activity in transferring the functionalized disaccharides carrying site-selectively modified azide, biotin, or fluorescent tags to antibodies without hydrolyzing the resulting transglycosylation products. This discovery, together with the excellent Fc deglycosylation activity of Endo-S2 on recombinant antibodies, allowed direct labeling and functionalization of antibodies in a one-pot manner without the need of intermediate and enzyme separation. The site-specific introduction of varied numbers of azide groups enabled a highly efficient synthesis of homogeneous antibody-drug conjugates (ADCs) with a precise control of the drug-to-antibody ratio (DAR) ranging from 2 to 12 via a copper-free strain-promoted click reaction. Cell viability assays showed that ADCs with higher DARs were more potent in killing antigen-overexpressed cells than the ADCs with lower DARs. This new method is expected to find applications not only for antibody-drug conjugation but also for cell labeling, imaging, and diagnosis.
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Affiliation(s)
- Xiao Zhang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Chong Ou
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Huiying Liu
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Sunaina Kiran Prabhu
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Qiang Yang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regents Drive, College Park, Maryland 20742, United States
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29
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Kang MS, Kong TWS, Khoo JYX, Loh TP. Recent developments in chemical conjugation strategies targeting native amino acids in proteins and their applications in antibody-drug conjugates. Chem Sci 2021; 12:13613-13647. [PMID: 34760149 PMCID: PMC8549674 DOI: 10.1039/d1sc02973h] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Many fields in chemical biology and synthetic biology require effective bioconjugation methods to achieve their desired functions and activities. Among such biomolecule conjugates, antibody-drug conjugates (ADCs) need a linker that provides a stable linkage between cytotoxic drugs and antibodies, whilst conjugating in a biologically benign, fast and selective fashion. This review focuses on how the development of novel organic synthesis can solve the problems of traditional linker technology. The review shall introduce and analyse the current developments in the modification of native amino acids on peptides or proteins and their applicability to ADC linker. Thereafter, the review shall discuss in detail each endogenous amino acid's intrinsic reactivity and selectivity aspects, and address the research effort to construct an ADC using each conjugation method.
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Affiliation(s)
- Min Sun Kang
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Theresa Wai See Kong
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Joycelyn Yi Xin Khoo
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
| | - Teck-Peng Loh
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University 21 Nanyang Link 637371 Singapore
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30
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Xu L, Silva MJSA, Gois PMP, Kuan SL, Weil T. Chemoselective cysteine or disulfide modification via single atom substitution in chloromethyl acryl reagents. Chem Sci 2021; 12:13321-13330. [PMID: 34777751 PMCID: PMC8528048 DOI: 10.1039/d1sc03250j] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
The development of bioconjugation chemistry has enabled the combination of various synthetic functionalities to proteins, giving rise to new classes of protein conjugates with functions well beyond what Nature can provide. Despite the progress in bioconjugation chemistry, there are no reagents developed to date where the reactivity can be tuned in a user-defined fashion to address different amino acid residues in proteins. Here, we report that 2-chloromethyl acryl reagents can serve as a simple yet versatile platform for selective protein modification at cysteine or disulfide sites by tuning their inherent electronic properties through the amide or ester linkage. Specifically, the 2-chloromethyl derivatives (acrylamide or acrylate) can be obtained via a simple and easily implemented one-pot reaction based on the coupling reaction between commercially available starting materials with different end-group functionalities (amino group or hydroxyl group). 2-Chloromethyl acrylamide reagents with an amide linkage favor selective modification at the cysteine site with fast reaction kinetics and near quantitative conversations. In contrast, 2-chloromethyl acrylate reagents bearing an ester linkage can undergo two successive Michael reactions, allowing the selective modification of disulfides bonds with high labeling efficiency and good conjugate stability. 2-Chloromethyl acryl derivatives (acrylamides and acrylates) can serve as simple and versatile bioconjugation reagents to achieve site-selective cysteine and disulfide modification on demand and with high efficiency.![]()
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Affiliation(s)
- Lujuan Xu
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany .,Institute of Inorganic Chemistry I, Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Maria J S A Silva
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa 1649-003 Lisbon Portugal
| | - Pedro M P Gois
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa 1649-003 Lisbon Portugal
| | - Seah Ling Kuan
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany .,Institute of Inorganic Chemistry I, Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research Ackermannweg 10 55128 Mainz Germany .,Institute of Inorganic Chemistry I, Ulm University Albert-Einstein-Allee 11 89081 Ulm Germany
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31
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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32
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Zhu F, Powell WC, Jing R, Walczak MA. Organometallic Ala M Reagents for Umpolung Peptide Diversification. CHEM CATALYSIS 2021; 1:870-884. [PMID: 34738092 PMCID: PMC8562471 DOI: 10.1016/j.checat.2021.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Selective modifications of peptides and proteins have emerged as a promising strategy to develop novel mechanistic probes and prepare compounds with translational potentials. Here, we report alanine carbastannatranes AlaSn as a universal synthon in various C-C and C-heteroatom bond-forming reactions. These reagents are compatible with peptide manipulation techniques and can undergo chemoselective conjugation in minutes when promoted by Pd(0). Despite their increased nucleophilicity and propensity to transfer the alkyl group, C(sp3)-C(sp2) coupling with AlaSn can be accomplished at room temperature under buffered conditions (pH 6.5-8.5). We also show that AlaSn can be easily transformed into several canonical L- and D-amino acids in arylation, acylation, and etherification reactions. Furthermore, AlaSn can partake in macrocyclizations exemplified by the synthesis of medium size cyclic peptides with various topologies. Taken together, metalated alanine AlaSn demonstrates unparalleled scope and represents a new type of umpolung reagents suitable for structure-activity relationship studies and peptide diversification.
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Affiliation(s)
- Feng Zhu
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, P. R. C
- These authors contributed equally
| | - Wyatt C. Powell
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
- These authors contributed equally
| | - Ruiheng Jing
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Maciej A. Walczak
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
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33
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Ou C, Li C, Zhang R, Yang Q, Zong G, Dai Y, Francis RL, Bournazos S, Ravetch JV, Wang LX. One-Pot Conversion of Free Sialoglycans to Functionalized Glycan Oxazolines and Efficient Synthesis of Homogeneous Antibody-Drug Conjugates through Site-Specific Chemoenzymatic Glycan Remodeling. Bioconjug Chem 2021; 32:1888-1897. [PMID: 34351736 DOI: 10.1021/acs.bioconjchem.1c00314] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Antibody-drug conjugates (ADCs) are an important class of therapeutic agents that harness the highly specific antigen targeting property of antibodies to deliver toxic drugs for targeted cell killing. Site-specific conjugation methods are highly desirable for constructing homogeneous ADCs that possess a well-defined antibody-to-drug ratio, stability, ideal pharmacological profile, and optimal therapeutic index. We report here a facile synthesis of functionalized glycan oxazolines from free sialoglycans that are key donor substrates for enzymatic Fc glycan remodeling and the application of an efficient endoglycosidase mutant (Endo-S2 D184M) for site-specific glycan transfer to construct homogeneous ADCs. We found that by a sequential use of two coupling reagents under optimized conditions, free sialoglycans could be efficiently converted to selectively functionalized glycan oxazolines carrying azide-, cyclopropene-, and norbornene-tags, respectively, in excellent yield and in a simple one-pot manner. We further demonstrated that the recently reported Endo-S2 D184 M mutant was highly efficient for Fc glycan remodeling with the selectively modified glycan oxazolines to introduce tags into an antibody, which required a significantly smaller amount of glycan oxazolines and a much shorter reaction time than that of the Endo-S D233Q-catalyzed reaction, thus minimizing the side reactions. Finally homogeneous ADCs were constructed with three different click reactions. The resulting ADCs showed excellent serum stability, and in vitro cytotoxicity assays indicated that all the three ADCs generated from the distinct click reactions possessed potent and comparable cytotoxicity for targeted cancer cell killing.
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Affiliation(s)
- Chong Ou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Roushu Zhang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Qiang Yang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Yuanwei Dai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Rebecca L Francis
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York 10065, United States
| | - Stylianos Bournazos
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York 10065, United States
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York 10065, United States
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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34
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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35
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Abstract
Click chemistry has been established rapidly as one of the most valuable methods for the chemical transformation of complex molecules. Due to the rapid rates, clean conversions to the products, and compatibility of the reagents and reaction conditions even in complex settings, it has found applications in many molecule-oriented disciplines. From the vast landscape of click reactions, approaches have emerged in the past decade centered around oxidative processes to generate in situ highly reactive synthons from dormant functionalities. These approaches have led to some of the fastest click reactions know to date. Here, we review the various methods that can be used for such oxidation-induced "one-pot" click chemistry for the transformation of small molecules, materials, and biomolecules. A comprehensive overview is provided of oxidation conditions that induce a click reaction, and oxidation conditions are orthogonal to other click reactions so that sequential "click-oxidation-click" derivatization of molecules can be performed in one pot. Our review of the relevant literature shows that this strategy is emerging as a powerful approach for the preparation of high-performance materials and the generation of complex biomolecules. As such, we expect that oxidation-induced "one-pot" click chemistry will widen in scope substantially in the forthcoming years.
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Affiliation(s)
- Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Floris van Delft
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,Synaffix BV, Industrielaan 63, 5349 AE, Oss, The Netherlands
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36
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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37
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Park Y, Baumann AL, Moon H, Byrne S, Kasper MA, Hwang S, Sun H, Baik MH, Hackenberger CPR. The mechanism behind enhanced reactivity of unsaturated phosphorus(v) electrophiles towards thiols. Chem Sci 2021; 12:8141-8148. [PMID: 34194704 PMCID: PMC8208129 DOI: 10.1039/d1sc01730f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Vinyl- and ethynyl phosphorus(v) electrophiles are a versatile class of thiol-reactive reagents suitable for cysteine-selective peptide and protein modifications, especially for the generation of antibody conjugates. Herein we investigated the reactivity of various P(v) reagents towards thiol addition. Complementing previous studies, we observed that the heteroatoms X (X = S, O, NH) as well as the vinyl- vs. ethynyl-substituent bound to phosphorus greatly influence the overall reactivity. These experimentally observed trends, as well as the high Z-selectivity for thiol additions to ethynyl derivatives, were further elucidated using DFT calculations. Hyperconjugation was a key means of stabilizing the intermediate generated upon the thiol addition, thus determining both the reactivity and stereoselectivity of unsaturated P(v) electrophiles. Specifically, the energetically low-lying σ antibonding orbital of the P–S bond more readily stabilizes the electron density from the lone pair (LP) of the generated carbanion, rendering the phosphonothiolates more reactive compared to the derivatives bearing oxygen and nitrogen. Our studies provide a detailed mechanistic picture for designing P(v)-based electrophiles with fine-tuned reactivity profiles. Computational analysis of different unsaturated phosphorus(v) electrophiles revealed a mechanistic picture to rationalize their selectivity and reactivity in cysteine-selective peptide and protein modifications.![]()
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Affiliation(s)
- Yerin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Alice L Baumann
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Hyejin Moon
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea
| | - Stephen Byrne
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Marc-André Kasper
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Songhwan Hwang
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Han Sun
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Mu-Hyun Baik
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS) Daejeon 34141 Republic of Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Christian P R Hackenberger
- Chemical Biology Department, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany .,Department of Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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38
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Tuang S, Dieppa-Matos D, Zhang C, Shugrue CR, Dai P, Loas A, Pentelute BL. A reactive peptide interface for site-selective cysteine bioconjugation. Chem Commun (Camb) 2021; 57:3227-3230. [PMID: 33645592 PMCID: PMC8048384 DOI: 10.1039/d1cc00095k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report aqueous, site-selective modification of proteins using a reactive peptide interface comprising a nine-residue sequence. This interface is the fastest (second-order rate constant of 152 M-1 s-1) catalyst-free, cysteine-based method for modifying proteins available to date, and enables near-quantitative labeling of antibodies in cell lysate.
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Affiliation(s)
- Suan Tuang
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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39
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Huang J, Zhao R, Mo J, Wang F, Weng X, Zhou X. N 3 -Kethoxal-Based Bioorthogonal Intracellular RNA Labeling. Chembiochem 2021; 22:1559-1562. [PMID: 33393712 DOI: 10.1002/cbic.202000755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Indexed: 11/11/2022]
Abstract
There is growing interest in developing intracellular RNA tools. Herein, we describe a strategy for N3 -kethoxal (N3 K)-based bioorthogonal intracellular RNA functionalization. With N3 K labeling followed by an in vivo click reaction with DBCO derivatives, RNA can be modified with fluorescent or phenol groups. This strategy provides a new way of labeling RNA inside cells.
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Affiliation(s)
- Jinguo Huang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Ruiqi Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, 430072, P. R. China
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40
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Wijetunge AN, Davis GJ, Shadmehr M, Townsend JA, Marty MT, Jewett JC. Copper-Free Click Enabled Triazabutadiene for Bioorthogonal Protein Functionalization. Bioconjug Chem 2021; 32:254-258. [PMID: 33492934 DOI: 10.1021/acs.bioconjchem.0c00677] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aryl diazonium ions have long been used in bioconjugation due to their reactivity toward electron-rich aryl residues, such as tyrosine. However, their utility in biological systems has been restricted due to the requirement of harsh conditions for their generation in situ, as well as limited hydrolytic stability. Previous work describing a scaffold known as triazabutadiene (TBD) has shown the ability to protect aryl diazonium ions allowing for increased synthetic utility, as well as triggered release under biologically relevant conditions. Herein, we describe the synthesis and application of a novel TBD, capable of installation of a cyclooctyne on protein surfaces for later use of copper-free click reactions involving functional azides. The probe shows efficient protein labeling across a wide pH range that can be accomplished in a convenient and timely manner. Orthogonality of the cyclooctyne modification was showcased by labeling a model protein in the presence of hen egg proteins, using an azide-containing fluorophore. We further confirmed that the azobenzene modification can be cleaved using sodium dithionite treatment.
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Affiliation(s)
- Anjalee N Wijetunge
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Garrett J Davis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Mehrdad Shadmehr
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Julia A Townsend
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - John C Jewett
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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41
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Walsh SJ, Bargh JD, Dannheim FM, Hanby AR, Seki H, Counsell AJ, Ou X, Fowler E, Ashman N, Takada Y, Isidro-Llobet A, Parker JS, Carroll JS, Spring DR. Site-selective modification strategies in antibody-drug conjugates. Chem Soc Rev 2021; 50:1305-1353. [PMID: 33290462 DOI: 10.1039/d0cs00310g] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibody-drug conjugates (ADCs) harness the highly specific targeting capabilities of an antibody to deliver a cytotoxic payload to specific cell types. They have garnered widespread interest in drug discovery, particularly in oncology, as discrimination between healthy and malignant tissues or cells can be achieved. Nine ADCs have received approval from the US Food and Drug Administration and more than 80 others are currently undergoing clinical investigations for a range of solid tumours and haematological malignancies. Extensive research over the past decade has highlighted the critical nature of the linkage strategy adopted to attach the payload to the antibody. Whilst early generation ADCs were primarily synthesised as heterogeneous mixtures, these were found to have sub-optimal pharmacokinetics, stability, tolerability and/or efficacy. Efforts have now shifted towards generating homogeneous constructs with precise drug loading and predetermined, controlled sites of attachment. Homogeneous ADCs have repeatedly demonstrated superior overall pharmacological profiles compared to their heterogeneous counterparts. A wide range of methods have been developed in the pursuit of homogeneity, comprising chemical or enzymatic methods or a combination thereof to afford precise modification of specific amino acid or sugar residues. In this review, we discuss advances in chemical and enzymatic methods for site-specific antibody modification that result in the generation of homogeneous ADCs.
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Affiliation(s)
- Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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42
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Kato M, Foley B, Vu J, Huynh M, Lucero K, Harmon C, Cheruzel L. Promoting P450 BM3 heme domain dimerization with a tris(5-iodoacetamido-1,10-phenanthroline)Ru(II) complex. Biotechnol Appl Biochem 2020; 67:536-540. [PMID: 33376255 DOI: 10.1002/bab.1970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein dimerization often occurs in many biological systems as to provide structural and functional advantages. A tris(5-iodoacetamido-1,10-phenanthroline)Ruthenium(II) complex was shown to promote the covalent dimerization of a P450 BM3 heme domain mutant containing a surface exposed non-native single cysteine residue. The formation of homodimeric species was confirmed by protein gel electrophoresis, mass spectrometry and UV-Vis spectroscopy. The dimeric species could be separated from the monomer and aggregates by size-exclusion chromatography. Docking simulation reveals a plausible structure with two proteins covalently conjugated to the inorganic compound.
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Affiliation(s)
- Mallory Kato
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Bridget Foley
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Julia Vu
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Michael Huynh
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Kathreena Lucero
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Caroline Harmon
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
| | - Lionel Cheruzel
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101
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43
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Janson N, Krüger T, Karsten L, Boschanski M, Dierks T, Müller KM, Sewald N. Bifunctional Reagents for Formylglycine Conjugation: Pitfalls and Breakthroughs. Chembiochem 2020; 21:3580-3593. [PMID: 32767537 PMCID: PMC7756428 DOI: 10.1002/cbic.202000416] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/05/2020] [Indexed: 12/28/2022]
Abstract
Formylglycine-generating enzymes specifically oxidize cysteine within the consensus sequence CxPxR to Cα -formylglycine (FGly). This noncanonical electrophilic amino acid can subsequently be addressed selectively by bioorthogonal hydrazino-iso-Pictet-Spengler (HIPS) or Knoevenagel ligation to attach payloads like fluorophores or drugs to proteins to obtain a defined payload-to-protein ratio. However, the disadvantages of these conjugation techniques include the need for a large excess of conjugation building block, comparably low reaction rates and limited stability of FGly-containing proteins. Therefore, functionalized clickable HIPS and tandem Knoevenagel building blocks were synthesized, conjugated to small proteins (DARPins) and subsequently linked to strained alkyne-containing payloads for protein labeling. This procedure allowed the selective bioconjugation of one or two DBCO-carrying payloads with nearly stoichiometric amounts at low concentrations. Furthermore, an azide-modified tandem Knoevenagel building block enabled the synthesis of branched PEG linkers and the conjugation of two fluorophores, resulting in an improved signal-to-noise ratio in live-cell fluorescence-imaging experiments targeting the EGF receptor.
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Affiliation(s)
- Nils Janson
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Tobias Krüger
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Lennard Karsten
- Cellular and Molecular BiotechnologyBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Mareile Boschanski
- Faculty of ChemistryBiochemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Thomas Dierks
- Faculty of ChemistryBiochemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Kristian M. Müller
- Cellular and Molecular BiotechnologyBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Norbert Sewald
- Faculty of ChemistryOrganic and Bioorganic ChemistryBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
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44
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Ando T, Takamori Y, Yokoyama T, Yamamoto M, Kawakami T. Directed evolution of dibenzocyclooctyne-reactive peptide tags for protein labeling. Biochem Biophys Res Commun 2020; 534:27-33. [PMID: 33310184 DOI: 10.1016/j.bbrc.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023]
Abstract
Protein labeling with a functional molecule is a technique widely used for protein research. The covalent reaction of self-labeling peptide tags with synthetic probe-modified small molecules enables tag-fused protein labeling with chemically diverse molecules, including fluorescent probes. We report the discovery, by in vitro directed evolution, of a novel 23-mer dibenzocyclooctyne (DBCO)-reactive peptide (DRP) tag using Systematic Evolution of Ligands by EXponential enrichment (SELEX) with a combination of a reconstituted cell-free translation system (PURE system) and cDNA display. The N- and C-terminal DRP truncations created a shorter 16-mer DBCO-reactive peptide (sDRP) tag without significant reactivity reduction. By fusing the sDRP tag to a model protein, we showed the chemical labeling and in-gel fluorescence imaging of the sDRP-fused protein using a fluorescent DBCO probe. Results showed that sDRP tag-mediated protein labeling has potential for use as a basic molecular tool in a variety of applications for protein research.
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Affiliation(s)
- Takehiro Ando
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Yukio Takamori
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takumi Yokoyama
- Department of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Mizuki Yamamoto
- Department of Integrated Applied Life Science, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan
| | - Takashi Kawakami
- Faculty of Life and Environmental Sciences, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi, 400-8510, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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45
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Recent advances of thiol-selective bioconjugation reactions. Curr Opin Chem Biol 2020; 58:28-36. [DOI: 10.1016/j.cbpa.2020.04.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/09/2023]
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46
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Selective Covalent Targeting of Anti-apoptotic BFL-1 by a Sulfonium-Tethered Peptide. Chembiochem 2020; 22:340-344. [PMID: 32790056 DOI: 10.1002/cbic.202000473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Indexed: 12/21/2022]
Abstract
Anti-apoptotic B cell lymphoma 2 (BCL-2) family proteins are proven targets for human cancers. Targeting the BH3-binding pockets of these anti-apoptotic proteins could reactivate apoptosis in BCL-2-depedent cancers. BFL-1 is a BCL-2 family protein overexpressed in various chemoresistant cancers. A unique cysteine at the binding interface of the BH3 and BFL-1 was previously proven to be an intriguing targeting site to irreversibly inhibit BFL-1 functions with stabilized cyclic peptide bearing a covalent warhead. Recently, we developed a sulfonium-tethered peptide cyclization strategy to construct peptide ligands that could selectively and efficiently react with the cysteine(s) of target proteins near the interacting interface. Using this method, we constructed a BFL-1 peptide inhibitor, B4-MC, that could selectively conjugate with BFL-1 both in vitro and in cell. B4-MC showed good cellular uptake, colocalized with BFL-1 on mitochondria, and showed obvious growth inhibition of BFL-1 over-expressed cancer cell lines.
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47
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48
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Doh JK, Tobin SJ, Beatty KE. MiniVIPER Is a Peptide Tag for Imaging and Translocating Proteins in Cells. Biochemistry 2020; 59:3051-3059. [PMID: 32786411 DOI: 10.1021/acs.biochem.0c00526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Microscopy allows researchers to interrogate proteins within a cellular context. To deliver protein-specific contrast, we developed a new class of genetically encoded peptide tags called versatile interacting peptide (VIP) tags. VIP tags deliver a reporter to a target protein via the formation of a heterodimer between the peptide tag and an exogenously added probe peptide. We report herein a new VIP tag named MiniVIPER, which is comprised of a MiniE-MiniR heterodimer. We first demonstrated the selectivity of MiniVIPER by labeling three cellular targets: transferrin receptor 1 (TfR1), histone protein H2B, and the mitochondrial protein TOMM20. We showed that either MiniE or MiniR could serve as the genetically encoded tag. Next, we demonstrated MiniVIPER's versatility by generating five spectrally distinct probe peptides to label tagged TfR1 on live cells. Lastly, we demonstrated two new applications for VIP tags. First, we used MiniVIPER in combination with another VIP tag, VIPER, to selectively label two different proteins in a single cell (e.g., TfR1 with H2B or TOMM20). Second, we used MiniVIPER to translocate a fluorescent protein to the nucleus through in situ dimerization of mCherry with H2B-mEmerald. In summary, MiniVIPER is a new peptide tag that enables multitarget imaging and artificial dimerization of proteins in cells.
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Affiliation(s)
- Julia K Doh
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Savannah J Tobin
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Kimberly E Beatty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon 97239, United States
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Jiang T, Laughlin ST. Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation. Methods Enzymol 2020; 641:1-34. [PMID: 32713519 DOI: 10.1016/bs.mie.2020.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.
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Affiliation(s)
- Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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50
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Pomplun S, Shugrue CR, Schmitt AM, Schissel CK, Farquhar CE, Pentelute BL. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Christopher R. Shugrue
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | | | - Carly K. Schissel
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Charlotte E. Farquhar
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
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