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Yi S, Wei S, Wu Q, Wang H, Yao Z. Azaphilones as Activation‐Free Primary‐Amine‐Specific Bioconjugation Reagents for Peptides, Proteins and Lipids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shandong Yi
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Siyuan Wei
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Qingsong Wu
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Zhu‐Jun Yao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing Jiangsu 210023 China
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2
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Tang KC, Cao J, Boatner LM, Li L, Farhi J, Houk KN, Spangle J, Backus KM, Raj M. Tunable Amine-Reactive Electrophiles for Selective Profiling of Lysine. Angew Chem Int Ed Engl 2022; 61:e202112107. [PMID: 34762358 PMCID: PMC10111338 DOI: 10.1002/anie.202112107] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/19/2021] [Indexed: 12/26/2022]
Abstract
Proteome profiling by activated esters identified >9000 ligandable lysines but they are limited as covalent inhibitors due to poor hydrolytic stability. Here we report our efforts to design and discover a new series of tunable amine-reactive electrophiles (TAREs) for selective and robust labeling of lysine. The major challenges in developing selective probes for lysine are the high nucleophilicity of cysteines and poor hydrolytic stability. Our work circumvents these challenges by a unique design of the TAREs that form stable adducts with lysine and on reaction with cysteine generate another reactive electrophiles for lysine. We highlight that TAREs exhibit substantially high hydrolytic stability as compared to the activated esters and are non-cytotoxic thus have the potential to act as covalent ligands. We applied these alternative TAREs for the intracellular labeling of proteins in different cell lines, and for the selective identification of lysines in the human proteome on a global scale.
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Affiliation(s)
- Kuei-Chien Tang
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Jian Cao
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M Boatner
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
- Present address: Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Linwei Li
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Jonathan Farhi
- Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - Jennifer Spangle
- Department of Radiation Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Keriann M Backus
- Department of Chemistry and Biochemistry, College of Arts and Sciences, UCLA, Los Angeles, CA, 90095, USA
- Present address: Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Monika Raj
- Present address: Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
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3
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Tang K, Cao J, Boatner LM, Li L, Farhi J, Houk KN, Spangle J, Backus KM, Raj M. Tunable Amine‐Reactive Electrophiles for Selective Profiling of Lysine. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kuei‐Chien Tang
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Jian Cao
- Department of Chemistry and Biochemistry College of Arts and Sciences UCLA Los Angeles CA 90095 USA
| | - Lisa M. Boatner
- Department of Chemistry and Biochemistry College of Arts and Sciences UCLA Los Angeles CA 90095 USA
- Present address: Department of Biological Chemistry David Geffen School of Medicine UCLA Los Angeles CA 90095 USA
| | - Linwei Li
- Department of Chemistry and Biochemistry College of Arts and Sciences UCLA Los Angeles CA 90095 USA
| | - Jonathan Farhi
- Department of Radiation Oncology Emory University Atlanta GA 30322 USA
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry College of Arts and Sciences UCLA Los Angeles CA 90095 USA
| | - Jennifer Spangle
- Department of Radiation Oncology Emory University Atlanta GA 30322 USA
| | - Keriann M. Backus
- Department of Chemistry and Biochemistry College of Arts and Sciences UCLA Los Angeles CA 90095 USA
- Present address: Department of Biological Chemistry David Geffen School of Medicine UCLA Los Angeles CA 90095 USA
| | - Monika Raj
- Present address: Department of Chemistry Emory University Atlanta GA 30322 USA
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4
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Yi S, Wei S, Wu Q, Wang H, Yao ZJ. Azaphilones as Activation-Free Primary-Amine-Specific Bioconjugation Reagents for Peptides, Proteins and Lipids. Angew Chem Int Ed Engl 2021; 61:e202111783. [PMID: 34825445 DOI: 10.1002/anie.202111783] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 01/11/2023]
Abstract
Residue-selective bioconjugation methods for biomolecules are highly sought to expand the scope of their biological and medical applications. Inspired by the mechanism of the generation of natural vinylogous γ-pyridones (vPDNs), we have developed a novel unique azaphilone-based, activation-free primary-amine-selective bioconjugation method for biomolecules. Our strategy allows facile functionalization of primary amine groups in peptides and proteins, including the clinically used therapeutic antibody trastuzumab, by generating a highly stable vPDN linkage. Excellent chemoselectivity toward primary amines also enables the azaphilone derivatives to specifically modify the lipid components of Gram-positive bacteria while bypassing Gram-negative bacteria and mammalian cells. The new method shows significant advantages including chemoselectivity, efficiency, flexibility and biocompatibility, and therefore provides a valuable addition to the current toolbox for biomolecule conjugation.
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Affiliation(s)
- Shandong Yi
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Siyuan Wei
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Qingsong Wu
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Zhu-Jun Yao
- State Key Laboratory of Coordination Chemistry and Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
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5
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Laserna V, Abegg D, Afonso CF, Martin EM, Adibekian A, Ravn P, Corzana F, Bernardes GJL. Dichloro Butenediamides as Irreversible Site‐Selective Protein Conjugation Reagent. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Victor Laserna
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 USA
| | - Cláudia F. Afonso
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Esther M. Martin
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building Granta Park Cambridge CB21 6GH UK
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 USA
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building Granta Park Cambridge CB21 6GH UK
- Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark
| | - Francisco Corzana
- Departamento de Química Centro de Investigación en Síntesis Química Universidad de La Rioja 26006 Logroño Spain
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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Laserna V, Abegg D, Afonso CF, Martin EM, Adibekian A, Ravn P, Corzana F, Bernardes GJL. Dichloro Butenediamides as Irreversible Site-Selective Protein Conjugation Reagent. Angew Chem Int Ed Engl 2021; 60:23750-23755. [PMID: 34472678 PMCID: PMC8596790 DOI: 10.1002/anie.202108791] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Indexed: 01/21/2023]
Abstract
We describe maleic-acid derivatives as robust cysteine-selective reagents for protein labelling with comparable kinetics and superior stability relative to maleimides. Diamide and amido-ester derivatives proved to be efficient protein-labelling species with a common mechanism in which a spontaneous cyclization occurs upon addition to cysteine. Introduction of chlorine atoms in their structures triggers ring hydrolysis or further conjugation with adjacent residues, which results in conjugates that are completely resistant to retro-Michael reactions in the presence of biological thiols and human plasma. By controlling the microenvironment of the reactive site, we can control selectivity towards the hydrolytic pathway, forming homogeneous conjugates. The method is applicable to several scaffolds and enables conjugation of different payloads. The synthetic accessibility of these reagents and the mild conditions required for fast and complete conjugation together with the superior stability of the conjugates make this strategy an important alternative to maleimides in bioconjugation.
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Affiliation(s)
- Victor Laserna
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Fl, 33458, USA
| | - Cláudia F Afonso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Esther M Martin
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Fl, 33458, USA
| | - Peter Ravn
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.,Department of Biotherapeutic Discovery, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006, Logroño, Spain
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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7
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Alvarez Dorta D, Deniaud D, Mével M, Gouin SG. Tyrosine Conjugation Methods for Protein Labelling. Chemistry 2020; 26:14257-14269. [DOI: 10.1002/chem.202001992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/09/2020] [Indexed: 12/23/2022]
Affiliation(s)
| | - David Deniaud
- CNRS, CEISAM UMR, 6230 Université de Nantes 44000 Nantes France
| | - Mathieu Mével
- CHU de Nantes, INSERM UMR 1089 Université de Nantes 44200 Nantes France
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8
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Lim D, Wen X, Seebeck FP. Selenoimidazolium Salts as Supramolecular Reagents for Protein Alkylation. Chembiochem 2020; 21:3515-3520. [DOI: 10.1002/cbic.202000557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/15/2022]
Affiliation(s)
- David Lim
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a Basel 4002 Switzerland
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Hansen BK, Loveridge CJ, Thyssen S, Wørmer GJ, Nielsen AD, Palmfeldt J, Johannsen M, Poulsen TB. STEFs: Activated Vinylogous Protein-Reactive Electrophiles. Angew Chem Int Ed Engl 2019; 58:3533-3537. [DOI: 10.1002/anie.201814073] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/04/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Bente K. Hansen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | | | - Stine Thyssen
- Department of Forensic Medicine; Aarhus University; Palle Juul-Jensens Boulevard 99 8200 Aarhus N Denmark
| | - Gustav J. Wørmer
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | - Andreas D. Nielsen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine-Research Unit for Molecular Medicine; Aarhus University hospital; Palle Juul-Jensens Boulevard 82 8200 Aarhus N Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine; Aarhus University; Palle Juul-Jensens Boulevard 99 8200 Aarhus N Denmark
| | - Thomas B. Poulsen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
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10
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Hansen BK, Loveridge CJ, Thyssen S, Wørmer GJ, Nielsen AD, Palmfeldt J, Johannsen M, Poulsen TB. STEFs: Activated Vinylogous Protein-Reactive Electrophiles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bente K. Hansen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | | | - Stine Thyssen
- Department of Forensic Medicine; Aarhus University; Palle Juul-Jensens Boulevard 99 8200 Aarhus N Denmark
| | - Gustav J. Wørmer
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | - Andreas D. Nielsen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine-Research Unit for Molecular Medicine; Aarhus University hospital; Palle Juul-Jensens Boulevard 82 8200 Aarhus N Denmark
| | - Mogens Johannsen
- Department of Forensic Medicine; Aarhus University; Palle Juul-Jensens Boulevard 99 8200 Aarhus N Denmark
| | - Thomas B. Poulsen
- Department of Chemistry; Aarhus University; Langelandsgade 140 8000 Aarhus C Denmark
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11
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Pettinger J, Jones K, Cheeseman MD. Lysine-Targeting Covalent Inhibitors. Angew Chem Int Ed Engl 2017; 56:15200-15209. [PMID: 28853194 DOI: 10.1002/anie.201707630] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Indexed: 12/11/2022]
Abstract
Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small-molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding-site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ-amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Matthew D Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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12
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Matthew D. Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
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13
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Bellucci JJ, Bhattacharyya J, Chilkoti A. A Noncanonical Function of Sortase Enables Site-Specific Conjugation of Small Molecules to Lysine Residues in Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Bellucci JJ, Bhattacharyya J, Chilkoti A. A noncanonical function of sortase enables site-specific conjugation of small molecules to lysine residues in proteins. Angew Chem Int Ed Engl 2014; 54:441-5. [PMID: 25363491 DOI: 10.1002/anie.201408126] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/17/2014] [Indexed: 11/09/2022]
Abstract
We provide the first demonstration that isopeptide ligation, a noncanonical activity of the enzyme sortase A, can be used to modify recombinant proteins. This reaction was used in vitro to conjugate small molecules to a peptide, an engineered targeting protein, and a full-length monoclonal antibody with an exquisite level of control over the site of conjugation. Attachment to the protein substrate occurred exclusively through isopeptide bonds at a lysine ε-amino group within a specific amino acid sequence. This reaction allows more than one molecule to be site-specifically conjugated to a protein at internal sites, thereby overcoming significant limitations of the canonical native peptide ligation reaction catalyzed by sortase A. Our method provides a unique chemical ligation procedure that is orthogonal to existing methods, supplying a new method to site-specifically modify lysine residues that will be a valuable addition to the protein conjugation toolbox.
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Affiliation(s)
- Joseph J Bellucci
- Department of Biomedical Engineering, Duke University, Durham, NC 27708 (USA) http://www.chilkotilab.pratt.duke.edu
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