1
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Huang W, Wen K, Laughlin ST, Escorihuela J. Unveiling the reactivity of 2 H-(thio)pyran-2-(thi)ones in cycloaddition reactions with strained alkynes through density functional theory studies. Org Biomol Chem 2024; 22:8285-8292. [PMID: 39302140 DOI: 10.1039/d4ob01263a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Over the past two decades, click chemistry transformations have revolutionized chemical and biological sciences. Among the different strain-promoted cycloadditions, the inverse electron demand Diels-Alder reaction (IEDDA) has been established as a benchmark reaction. We have theoretically investigated the IEDDA reaction of endo-bicyclo[6.1.0]nonyne (endo-BCN) with 2H-pyran-2-one, 2H-thiopyran-2-one, 2H-pyran-2-thione and 2H-thiopyran-2-thione. These 2H-(thio)pyran-2-(thi)ones have displayed different reactivity towards endo-BCN. Density functional theory (DFT) calculations show, in agreement with experiments, that endo-BCN reacts significantly faster with 2H-thiopyran-2-one compared to other 2H-(thio)pyran-2-(thi)one derivatives because of the lower distortion energy. Experimentally determined second-order rate constants for the reaction of a 2H-pyran-2-thione with different strained derivatives, including a 1-methylcyclopropene derivative and several cycloalkynes (exo-BCN, (1R,8S)-bicyclo[6.1.0]non-4-yne-9,9-diyl)dimethanol, dibenzocycylooctyne and a light activatable silacycloheptyne, were used to validate the computational investigations and shed light on this reaction.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Kangqiao Wen
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11790, USA.
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain.
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2
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Shajan I, Rochet LNC, Tracey SR, Benazza R, Jackowska B, Hernandez-Alba O, Cianférani S, Scott CJ, van Delft FL, Chudasama V, Albada B. Modular Semisynthetic Approach to Generate T Cell-Dependent Bispecific Constructs from Recombinant IgG1 Antibodies. Bioconjug Chem 2024; 35. [PMID: 39284580 PMCID: PMC11487494 DOI: 10.1021/acs.bioconjchem.4c00309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/09/2024] [Accepted: 09/09/2024] [Indexed: 10/20/2024]
Abstract
Redirecting T cells to tumor cells by bispecific antibodies is an effective approach to treat cancer, and T cell-dependent bispecific antibodies (TDBAs) are an emerging class of potent immunotherapeutic agents. By simultaneously targeting antigens on tumor cells and T cells, T cells are activated to kill tumor cells. Herein, we report a platform to generate a novel class of 2:1 structure of T cell-dependent bispecific antibody with bivalency for HER2 receptors on tumor cells and monovalency for CD3 receptors on T cells. For this, we use a biogenic inverse electron-demand Diels-Alder (IEDDA) click reaction on genetically encoded tyrosine residues to install one TCO handle on therapeutically approved antibody trastuzumab. Subsequent TCO-tetrazine click with a tetrazine-functionalized CD3-binding Fab yields a 2:1 HER2 × CD3 TDBA that exhibits a tumor-killing capability at picomolar concentrations. Monovalency toward the CD3 receptor on T cells can lower the chances of cytokine release syndrome, which is a common side effect of such agents. Our semisynthetic approach can generate highly potent TDBA constructs in a few chemoenzymatic and synthetic steps.
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Affiliation(s)
- Irene Shajan
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
| | - Léa N. C. Rochet
- Department
of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, United Kingdom
| | - Shannon R. Tracey
- Patrick
G. Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Rania Benazza
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
- Infrastructure
Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Bianka Jackowska
- Patrick
G. Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Oscar Hernandez-Alba
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
- Infrastructure
Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
- Infrastructure
Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Christopher J. Scott
- Patrick
G. Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
- Synaffix
BV—A Lonza Company, Kloosterstraat 9, Oss 5349 AB, The Netherlands
| | - Vijay Chudasama
- Department
of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, United Kingdom
| | - Bauke Albada
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
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3
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Fang Y, Hillman AS, Fox JM. Advances in the Synthesis of Bioorthogonal Reagents: s-Tetrazines, 1,2,4-Triazines, Cyclooctynes, Heterocycloheptynes, and trans-Cyclooctenes. Top Curr Chem (Cham) 2024; 382:15. [PMID: 38703255 PMCID: PMC11559631 DOI: 10.1007/s41061-024-00455-y] [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: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 05/06/2024]
Abstract
Aligned with the increasing importance of bioorthogonal chemistry has been an increasing demand for more potent, affordable, multifunctional, and programmable bioorthogonal reagents. More advanced synthetic chemistry techniques, including transition-metal-catalyzed cross-coupling reactions, C-H activation, photoinduced chemistry, and continuous flow chemistry, have been employed in synthesizing novel bioorthogonal reagents for universal purposes. We discuss herein recent developments regarding the synthesis of popular bioorthogonal reagents, with a focus on s-tetrazines, 1,2,4-triazines, trans-cyclooctenes, cyclooctynes, hetero-cycloheptynes, and -trans-cycloheptenes. This review aims to summarize and discuss the most representative synthetic approaches of these reagents and their derivatives that are useful in bioorthogonal chemistry. The preparation of these molecules and their derivatives utilizes both classical approaches as well as the latest organic chemistry methodologies.
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Affiliation(s)
- Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
| | - Ashlyn S Hillman
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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4
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Keijzer JF, Albada B. DNA nanocrane-based catalysts for region-specific protein modification. Org Biomol Chem 2024; 22:1447-1452. [PMID: 38270061 DOI: 10.1039/d3ob02025h] [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: 01/26/2024]
Abstract
This paper describes the development and performance of catalytic DNA-based nanocranes for the controlled modification of wild-type proteins. We show that the position of the catalyst offers control over the region of modification, and that reversible interactions between the catalytic structure and thrombin enable trigger-responsive modification, even in cell lysate.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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5
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Dudchak R, Podolak M, Holota S, Szewczyk-Roszczenko O, Roszczenko P, Bielawska A, Lesyk R, Bielawski K. Click chemistry in the synthesis of antibody-drug conjugates. Bioorg Chem 2024; 143:106982. [PMID: 37995642 DOI: 10.1016/j.bioorg.2023.106982] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Antibody-Drug Conjugates (ADC) are a new class of anticancer therapeutics with immense potential. They have been rapidly advancing in the last two decades. This fast speed of development has become possible due to several new technologies and methods. One of them is Click Chemistry, an approach that was created only two decades ago, but already is actively utilized for bioconjugation, material science and drug discovery. In this review, we researched the impact of Click Chemistry reactions on the synthesis and development of ADCs. The information about the most frequently utilized reactions, such as Michael's addition, Copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC), Strain-promoted azide-alkyne [3+2] cycloaddition (SPAAC), oxime bond formation, hydrazine-iso-Pictet-Spengler Ligation (HIPS), Diels-Alder reactions have been summarized. The implementation of thiol-maleimide Click Chemistry reaction in the synthesis of numerous FDA-approved Antibody-Drug Conjugates has been reported. The data amassed in the present review provides better understanding of the importance of Click Chemistry in the synthesis, development and improvement of the Antibody-Drug Conjugates and it will be helpful for further researches related to ADCs.
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Affiliation(s)
- Rostyslav Dudchak
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Magdalena Podolak
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Serhii Holota
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine
| | - Olga Szewczyk-Roszczenko
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Piotr Roszczenko
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Anna Bielawska
- Department of Biotechnology, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
| | - Roman Lesyk
- Department of Pharmaceutical, Organic and Bioorganic Chemistry, Danylo Halytsky Lviv National Medical University, Pekarska 69, Lviv 79010, Ukraine.
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Faculty of Pharmacy, Medical University of Bialystok, Jana Kilińskiego 1, Bialystok 15-089, Poland
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6
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Chen H, Wong HF, Qiu J, Li B, Yuan D, Kong H, Bao Y, Zhang Y, Xu Z, Tse YS, Xia J. Site-Selective Tyrosine Reaction for Antibody-Cell Conjugation and Targeted Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305012. [PMID: 38044303 PMCID: PMC10837340 DOI: 10.1002/advs.202305012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/27/2023] [Indexed: 12/05/2023]
Abstract
Targeted immunotherapies capitalize on the exceptional binding capabilities of antibodies to stimulate a host response that effectuates long-lived tumor destruction. One example is the conjugation of immunoglobulins (IgGs) to immune effector cells, which equips the cells with the ability to recognize and accurately kill malignant cells through a process called antibody-dependent cellular cytotoxicity (ADCC). In this study, a chemoenzymatic reaction is developed that specifically functionalizes a single tyrosine (Tyr, Y) residue, Y296, in the Fc domain of therapeutic IgGs. A one-pot reaction that combines the tyrosinase-catalyzed oxidation of tyrosine to o-quinone with a subsequent [3+2] photoaddition with vinyl ether is employed. This reaction installs fluorescent molecules or bioorthogonal groups at Y296 of IgGs or the C-terminal Y-tag of an engineered nanobody. The Tyr-specific reaction is utilized in constructing monofunctionalized antibody-drug conjugates (ADCs) and antibody/nanobody-conjugated effector cells, such as natural killer cells or macrophages. These results demonstrate the potential of site-selective antibody reactions for enhancing targeted cancer immunotherapy.
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Affiliation(s)
- Hongfei Chen
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Hong‐Chai Fabio Wong
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Jiaming Qiu
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Biquan Li
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Dingdong Yuan
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Hao Kong
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Yishu Bao
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Yu Zhang
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Zhiyi Xu
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Ying‐Lung Steve Tse
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Jiang Xia
- Department of ChemistryThe Chinese University of Hong KongShatinHong Kong SARChina
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7
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Bednar RM, Karplus PA, Mehl RA. Site-specific dual encoding and labeling of proteins via genetic code expansion. Cell Chem Biol 2023; 30:343-361. [PMID: 36977415 PMCID: PMC10764108 DOI: 10.1016/j.chembiol.2023.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/10/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023]
Abstract
The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.
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Affiliation(s)
- Riley M Bednar
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Agricultural and Life Sciences Building, Corvallis, OR 97331-7305, USA; GCE4All Research Center, Oregon State University, 2011 Agricultural and Life Sciences, Corvallis, OR 97331-7305, USA.
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8
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Rosenberger JE, Xie Y, Fang Y, Lyu X, Trout WS, Dmitrenko O, Fox JM. Ligand-Directed Photocatalysts and Far-Red Light Enable Catalytic Bioorthogonal Uncaging inside Live Cells. J Am Chem Soc 2023; 145:6067-6078. [PMID: 36881718 PMCID: PMC10589873 DOI: 10.1021/jacs.2c10655] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red light (660 nm) photocatalysis is used to initiate a cascade of DHTz oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially available conjugates of Hoechst dye (SiR-H) and docetaxel (SiR-T) are used to localize SiR to the nucleus and microtubules, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 μM SiR and 40 μM photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate-determining elimination step. In cellular studies, this uncaging process is successful at low concentrations of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as a photocatalyst and the fluorescent reporter for microtubule depolymerization, and with confocal microscopy, it was possible to visualize microtubule depolymerization in real time as the result of photocatalytic uncaging in live cells.
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Affiliation(s)
- Julia E. Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Olga Dmitrenko
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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9
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Dolan JP, Machin DC, Dedola S, Field RA, Webb ME, Turnbull WB. Synthesis of cholera toxin B subunit glycoconjugates using site-specific orthogonal oxime and sortase ligation reactions. Front Chem 2022; 10:958272. [PMID: 36186584 PMCID: PMC9515619 DOI: 10.3389/fchem.2022.958272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The chemoenzymatic synthesis of a series of dual N- and C-terminal-functionalized cholera toxin B subunit (CTB) glycoconjugates is described. Mucin 1 peptides bearing different levels of Tn antigen glycosylation [MUC1(Tn)] were prepared via solid-phase peptide synthesis. Using sortase-mediated ligation, the MUC1(Tn) epitopes were conjugated to the C-terminus of CTB in a well-defined manner allowing for high-density display of the MUC1(Tn) epitopes. This work explores the challenges of using sortase-mediated ligation in combination with glycopeptides and the practical considerations to obtain high levels of conjugation. Furthermore, we describe methods to combine two orthogonal labeling methodologies, oxime- and sortase-mediated ligation, to expand the biochemical toolkit and produce dual N- and C-terminal-labeled conjugates.
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Affiliation(s)
- Jonathan P. Dolan
- School of Chemistry and Astbury Centre of Structural Biology, University of Leeds, Leeds, United Kingdom
| | - Darren C. Machin
- School of Chemistry and Astbury Centre of Structural Biology, University of Leeds, Leeds, United Kingdom
| | | | - Robert A. Field
- Iceni Glycoscience Ltd., Norwich, United Kingdom
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Michael E. Webb
- School of Chemistry and Astbury Centre of Structural Biology, University of Leeds, Leeds, United Kingdom
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre of Structural Biology, University of Leeds, Leeds, United Kingdom
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10
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Jemas A, Xie Y, Pigga JE, Caplan JL, am Ende CW, Fox JM. Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light. J Am Chem Soc 2022; 144:1647-1662. [PMID: 35072462 PMCID: PMC9364228 DOI: 10.1021/jacs.1c10390] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
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Affiliation(s)
- Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jessica E. Pigga
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L. Caplan
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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11
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Keijzer JF, Albada B. DNA-assisted site-selective protein modification. Biopolymers 2021; 113:e23483. [PMID: 34878181 PMCID: PMC9285461 DOI: 10.1002/bip.23483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
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12
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Keijzer JF, Firet J, Albada B. Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates. Chem Commun (Camb) 2021; 57:12960-12963. [PMID: 34792071 DOI: 10.1039/d1cc05446e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two acyl-transfer catalysts were conjugated to thrombin-binding DNA aptamers to acylate thrombin. Modification occurred site-selectively on Lys (≫Ser) residues proximal to the respective aptamer-thrombin interface, was selective for thrombin in the presence of other proteins, and the activity of both DNA-catalysts could be controlled by an external trigger.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
| | - Judith Firet
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE, Wageningen, The Netherlands.
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13
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Bruins J, Damen JAM, Wijdeven MA, Lelieveldt LPWM, van Delft FL, Albada B. Non-Genetic Generation of Antibody Conjugates Based on Chemoenzymatic Tyrosine Click Chemistry. Bioconjug Chem 2021; 32:2167-2172. [PMID: 34519477 PMCID: PMC8532111 DOI: 10.1021/acs.bioconjchem.1c00351] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/30/2021] [Indexed: 12/01/2022]
Abstract
The availability of tools to generate homogeneous and stable antibody conjugates without recombinant DNA technology is a valuable asset in fields spanning from in vitro diagnostics to in vivo imaging and therapeutics. We present here a general approach for the conjugation to human IgG1 antibodies, by employing a straightforward two-stage protocol based on antibody deglycosylation followed by tyrosinase-mediated ortho-quinone strain-promoted click chemistry. The technology is validated by the efficient and clean generation of highly potent DAR2 and DAR4 antibody-drug conjugates (ADCs) with cytotoxic payloads MMAE or PBD dimer, and their in vitro evaluation.
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Affiliation(s)
- Jorick
J. Bruins
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Johannes A. M. Damen
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | | | | | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Synaffix
BV, Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Bauke Albada
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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14
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Wang C, Zhang H, Zhang T, Zou X, Wang H, Rosenberger J, Vannam R, Trout WS, Grimm JB, Lavis LD, Thorpe C, Jia X, Li Z, Fox JM. Enabling In Vivo Photocatalytic Activation of Rapid Bioorthogonal Chemistry by Repurposing Silicon-Rhodamine Fluorophores as Cytocompatible Far-Red Photocatalysts. J Am Chem Soc 2021; 143:10793-10803. [PMID: 34250803 PMCID: PMC8765119 DOI: 10.1021/jacs.1c05547] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromophores that absorb in the tissue-penetrant far-red/near-infrared window have long served as photocatalysts to generate singlet oxygen for photodynamic therapy. However, the cytotoxicity and side reactions associated with singlet oxygen sensitization have posed a problem for using long-wavelength photocatalysis to initiate other types of chemical reactions in biological environments. Herein, silicon-Rhodamine compounds (SiRs) are described as photocatalysts for inducing rapid bioorthogonal chemistry using 660 nm light through the oxidation of a dihydrotetrazine to a tetrazine in the presence of trans-cyclooctene dienophiles. SiRs have been commonly used as fluorophores for bioimaging but have not been applied to catalyze chemical reactions. A series of SiR derivatives were evaluated, and the Janelia Fluor-SiR dyes were found to be especially effective in catalyzing photooxidation (typically 3%). A dihydrotetrazine/tetrazine pair is described that displays high stability in both oxidation states. A protein that was site-selectively modified by trans-cyclooctene was quantitatively conjugated upon exposure to 660 nm light and a dihydrotetrazine. By contrast, a previously described methylene blue catalyst was found to rapidly degrade the protein. SiR-red light photocatalysis was used to cross-link hyaluronic acid derivatives functionalized by dihydrotetrazine and trans-cyclooctenes, enabling 3D culture of human prostate cancer cells. Photoinducible hydrogel formation could also be carried out in live mice through subcutaneous injection of a Cy7-labeled hydrogel precursor solution, followed by brief irradiation to produce a stable hydrogel. This cytocompatible method for using red light photocatalysis to activate bioorthogonal chemistry is anticipated to find broad applications where spatiotemporal control is needed in biological environments.
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Affiliation(s)
- Chuanqi Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - He Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Tao Zhang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xiaoyu Zou
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
| | - Hui Wang
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Julia Rosenberger
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Raghu Vannam
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - William S. Trout
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn Virginia, 20147, USA
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Xinqiao Jia
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
- Delaware Biotechnology Institute, Newark, Delaware 19711, USA
| | - Zibo Li
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, USA
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15
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Abstract
Cyclopentadiene is one of the most reactive dienes in normal electron-demand Diels-Alder reactions. The high reactivities and yields of cyclopentadiene cycloadditions make them ideal as click reactions. In this review, we discuss the history of the cyclopentadiene cycloaddition as well as applications of cyclopentadiene click reactions. Our emphasis is on experimental and theoretical studies on the reactivity and stability of cyclopentadiene and cyclopentadiene derivatives.
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Affiliation(s)
- Brian J. Levandowski
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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16
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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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17
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Chowdhury A, Chatterjee S, Pongen A, Sarania D, Tripathi NM, Bandyopadhyay A. nSite-Selective, Chemical Modification of Protein at Aromatic Side Chain and Their Emergent Applications. Protein Pept Lett 2021; 28:788-808. [PMID: 33511938 DOI: 10.2174/0929866528666210129152535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/20/2020] [Indexed: 11/22/2022]
Abstract
Site-selective chemical modification of protein side chain has probed enormous opportunities in the fundamental understanding of cellular biology and therapeutic applications. Primarily, in the field of biopharmaceutical where formulation of bioconjugates is found to be potential medicine than an individual constituent. In this regard, Lysine and Cysteine are the most widely used endogenous amino acid for these purposes. Recently, the aromatic side chain residues (Trp, Tyr, and His) that are low abundant in protein have gained more attention in therapeutic applications due to their advantages of chemical reactivity and specificity. This review discusses the site-selective bioconjugation methods for aromatic side chains (Trp, Tyr and His) and highlights the developed strategies in the last three years, along with their applications. Also, the review highlights the prevalent methods published earlier. We have examined that metal-catalyzed and photocatalytic reactions are gaining more attention for bioconjugation, though their practical operation is under development. The review has been summarized with the future perspective of protein and peptide conjugations contemplating therapeutic applications and challenges.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Akumlong Pongen
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Dhanjit Sarania
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Nitesh Mani Tripathi
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
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18
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Macias‐Contreras M, Zhu L. The Collective Power of Genetically Encoded Protein/Peptide Tags and Bioorthogonal Chemistry in Biological Fluorescence Imaging. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Macias‐Contreras
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
| | - Lei Zhu
- Department of Chemistry and Biochemistry Florida State University 95 Chieftan Way Tallahassee FL 32306-4390 USA
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19
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Smeenk MLWJ, Agramunt J, Bonger KM. Recent developments in bioorthogonal chemistry and the orthogonality within. Curr Opin Chem Biol 2020; 60:79-88. [PMID: 33152604 DOI: 10.1016/j.cbpa.2020.09.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/09/2023]
Abstract
The emergence of bioorthogonal reactions has greatly advanced research in the fields of biology and medicine. They are not only valuable for labeling, tracking, and understanding biomolecules within living organisms, but also important for constructing advanced bioengineering and drug delivery systems. As the systems studied are increasingly complex, the simultaneous use of multiple bioorthogonal reactions is equally desirable. In this review, we take a look at the different bioorthogonal reactions that have recently been developed, the methods of cellular incorporation and the strategies to create orthogonality within the bioorthogonal landscape.
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Affiliation(s)
- Mike L W J Smeenk
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jordi Agramunt
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Kimberly M Bonger
- Department of Synthetic Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands.
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20
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Keijzer JF, Albada B. Site-Specific and Trigger-Activated Modification of Proteins by Means of Catalytic Hemin/G-quadruplex DNAzyme Nanostructures. Bioconjug Chem 2020; 31:2283-2287. [PMID: 32909740 PMCID: PMC7581286 DOI: 10.1021/acs.bioconjchem.0c00422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Catalytic
nanostructures have the potency to mimic enzymatic features.
In this paper, we show that the complex between hemin and G-quadruplex
DNA efficiently catalyzes the modification of proteins with N-methyl luminol derivatives. Final conversions are reached
within 15–30 min, and LC-MS analysis of tryptic digests of
the proteins shows that the reaction proceeds with chemoselectivity
for electron-rich aromatic residues (Tyr ≫ Trp), and the site-specificity
of the modification depends on the sequence and secondary structure
folding of the G-quadruplex nanostructure. Furthermore, the modification
can be applied on proteins with different biomedical functions, and
the nanostructure can be designed to contain a regulatory element
in order to regulate protein modification by an external stimulus.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
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21
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Pigga JE, Fox JM. Flow Photochemical Syntheses of trans-Cyclooctenes and trans-Cycloheptenes Driven by Metal Complexation. Isr J Chem 2020; 60:207-218. [PMID: 34108738 PMCID: PMC8186252 DOI: 10.1002/ijch.201900085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Indexed: 12/19/2022]
Abstract
trans-Cyclooctenes and trans-cycloheptenes have long been the subject of physical organic study, but the broader application had been limited by synthetic accessibility. This account describes the development of a general, flow photochemical method for the preparative synthesis of trans-cycloalkene derivatives. Here, photoisom erization takes place in a closed-loop flow reactor where the reaction mixture is continuously cycled through Ag(I) on silica gel. Selective complexation of the trans-isomer by Ag(I) during flow drives an otherwise unfavorable isomeric ratio toward the trans-isomer. Analogous photoreactions under batch-conditions are low yielding, and flow chemistry is necessary in order to obtain trans-cycloalkenes in preparatively useful yields. The applications of the method to bioorthogonal chemistry and stereospecific transannulation chemistry are described.
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Affiliation(s)
- Jessica E Pigga
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
| | - Joseph M Fox
- Department of Chemistry and Biochemistry University of Delaware, Newark DE 19716
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22
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Levinn CM, Cerda MM, Pluth MD. Activatable Small-Molecule Hydrogen Sulfide Donors. Antioxid Redox Signal 2020; 32:96-109. [PMID: 31554416 PMCID: PMC6918874 DOI: 10.1089/ars.2019.7841] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/21/2019] [Indexed: 12/11/2022]
Abstract
Significance: Hydrogen sulfide (H2S) is an important biological signaling molecule involved in many physiological processes. These diverse roles have led researchers to develop contemporary methods to deliver H2S under physiologically relevant conditions and in response to various stimuli. Recent Advances: Different small-molecule donors have been developed that release H2S under various conditions. Key examples include donors activated in response to hydrolysis, to endogenous species, such as thiols, reactive oxygen species, and enzymes, and to external stimuli, such as photoactivation and bio-orthogonal chemistry. In addition, an alternative approach to release H2S has utilized the catalyzed hydrolysis of carbonyl sulfide (COS) by carbonic anhydrase to generate libraries of activatable COS-based H2S donors. Critical Issues: Small-molecule H2S donors provide important research and pharmacological tools to perturb H2S levels. Key needs, both in the development and in the use of such donors, include access to new donors that respond to specific stimuli as well as donors with well-defined control compounds that allow for clear delineation of the impact of H2S delivery from other donor byproducts. Future Directions: The abundance of reported small-molecule H2S donors provides biologists and physiologists with a chemical toolbox to ask key biological questions and to develop H2S-related therapeutic interventions. Further investigation into different releasing efficiencies in biological contexts and a clear understanding of biological responses to donors that release H2S gradually (e.g., hours to days) versus donors that generate H2S quickly (e.g., seconds to minutes) is needed.
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Affiliation(s)
- Carolyn M. Levinn
- Department of Chemistry and Biochemistry, Materials Science Institute, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Matthew M. Cerda
- Department of Chemistry and Biochemistry, Materials Science Institute, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - Michael D. Pluth
- Department of Chemistry and Biochemistry, Materials Science Institute, Institute of Molecular Biology, University of Oregon, Eugene, Oregon
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23
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Bruins J, van de Wouw C, Wagner K, Bartels L, Albada B, van Delft FL. Highly Efficient Mono-Functionalization of Knob-in-Hole Antibodies with Strain-Promoted Click Chemistry. ACS OMEGA 2019; 4:11801-11807. [PMID: 31460288 PMCID: PMC6682001 DOI: 10.1021/acsomega.9b01727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/25/2019] [Indexed: 05/03/2023]
Abstract
Knob-in-hole antibodies can be utilized to introduce a single tag for chemo-enzymatic functionalization. By either introducing a single C-terminal sortase tag (sortase-tag expressed protein ligation) or tyrosine tag (G4Y), mono-functionalization of the monoclonal antibody trastuzumab was achieved rapidly and in high yields. This method was applied to selectively and efficiently introduce a single fluorescent tag, cytokine or single-chain variable fragment, as well as produce clean homo dimers of trastuzumab.
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Affiliation(s)
- Jorick
J. Bruins
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Criss van de Wouw
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Koen Wagner
- AIMM
Therapeutics, Meibergdreef
59, 1105 BA Amsterdam, The Netherlands
| | - Lina Bartels
- AIMM
Therapeutics, Meibergdreef
59, 1105 BA Amsterdam, The Netherlands
| | - Bauke Albada
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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24
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Hwang D, Nilchan N, Nanna AR, Li X, Cameron MD, Roush WR, Park H, Rader C. Site-Selective Antibody Functionalization via Orthogonally Reactive Arginine and Lysine Residues. Cell Chem Biol 2019; 26:1229-1239.e9. [PMID: 31231031 DOI: 10.1016/j.chembiol.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/23/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023]
Abstract
Homogeneous antibody-drug conjugates (ADCs) that use a highly reactive buried lysine (Lys) residue embedded in a dual variable domain (DVD)-IgG1 format can be assembled with high precision and efficiency under mild conditions. Here we show that replacing the Lys with an arginine (Arg) residue affords an orthogonal ADC assembly that is site-selective and stable. X-ray crystallography confirmed the location of the reactive Arg residue at the bottom of a deep pocket. As the Lys-to-Arg mutation is confined to a single residue in the heavy chain of the DVD-IgG1, heterodimeric assemblies that combine a buried Lys in one arm, a buried Arg in the other arm, and identical light chains, are readily assembled. Furthermore, the orthogonal conjugation chemistry enables the loading of heterodimeric DVD-IgG1s with two different cargos in a one-pot reaction and thus affords a convenient platform for dual-warhead ADCs and other multifaceted antibody conjugates.
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Affiliation(s)
- Dobeen Hwang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Napon Nilchan
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Alex R Nanna
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Xiaohai Li
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael D Cameron
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William R Roush
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - HaJeung Park
- X-Ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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25
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Levandowski BJ, Svatunek D, Sohr B, Mikula H, Houk KN. Secondary Orbital Interactions Enhance the Reactivity of Alkynes in Diels-Alder Cycloadditions. J Am Chem Soc 2019; 141:2224-2227. [PMID: 30693769 PMCID: PMC8830044 DOI: 10.1021/jacs.8b13088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
We
have investigated the inverse electron-demand Diels–Alder
reactions of trans-cyclooctene (TCO) and endo-bicyclo[6.1.0]nonyne (BCN) with a 1,2,4,5-tetrazine,
a cyclopentadienone, and an ortho-benzoquinone. Tetrazines
react significantly faster with TCO compared to BCN because the highest
occupied molecular orbital (HOMO) of TCO is significantly higher in
energy than the HOMO of BCN and there is less distortion of the tetrazine.
Despite the different HOMO energies, TCO and BCN have similar reactivities
toward cyclopentadienones, while BCN is significantly more reactive
than TCO in the cycloaddition with ortho-benzoquinone.
We find that the higher reactivity of BCN compared to TCO with ortho-benzoquinone is due to secondary orbital interactions
of the BCN HOMO-1 with the diene LUMO.
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Affiliation(s)
- Brian J Levandowski
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States.,Institute of Applied Synthetic Chemistry , TU Wien , 1110 Vienna , Austria
| | - Barbara Sohr
- Institute of Applied Synthetic Chemistry , TU Wien , 1110 Vienna , Austria
| | - Hannes Mikula
- Institute of Applied Synthetic Chemistry , TU Wien , 1110 Vienna , Austria
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
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26
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Bruins JJ, van de Wouw C, Keijzer JF, Albada B, van Delft FL. Inducible, Selective Labeling of Proteins via Enzymatic Oxidation of Tyrosine. Methods Mol Biol 2019; 2012:357-368. [PMID: 31161517 DOI: 10.1007/978-1-4939-9546-2_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteins can be labeled site-specifically and in inducible fashion by exposing a small peptide tag (G4Y) on any of its termini and activating the newly exposed tyrosine residue with the enzyme mushroom tyrosinase. The enzyme generates a quinone by oxidizing the tyrosine, which in turn can perform strain-promoted oxidation-controlled ortho-quinone cycloaddition (SPOCQ) with strained alkynes and alkenes, generating a stable conjugation product. Here, we describe a protocol to perform SPOCQ reaction on proteins, along with notes to optimize yield and reaction rates. Conjugation efficiencies of over 95% to antibodies have been reported using this protocol.
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Affiliation(s)
- Jorick J Bruins
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Criss van de Wouw
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands.
| | - Floris L van Delft
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, The Netherlands.
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27
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Cheng L, Kang X, Wang D, Gao Y, Yi L, Xi Z. The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation. Org Biomol Chem 2019; 17:5675-5679. [DOI: 10.1039/c9ob00528e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The one-pot nonhydrolysis Staudinger reaction and Staudinger or SPAAC ligation were used for producing a FRET-based dyad in living cells as a proof-of-concept study.
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Affiliation(s)
- Longhuai Cheng
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xueying Kang
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Dan Wang
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Yasi Gao
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
| | - Long Yi
- State Key Laboratory of Organic–Inorganic Composites and Beijing Key Laboratory of Bioprocess
- Beijing University of Chemical Technology (BUCT)
- Beijing 100029
- China
- Collaborative Innovation Center of Chemical Science and Engineering
| | - Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology
- National Engineering Research Center of Pesticide (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
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Svatunek D, Houszka N, Hamlin TA, Bickelhaupt FM, Mikula H. Chemoselectivity of Tertiary Azides in Strain-Promoted Alkyne-Azide Cycloadditions. Chemistry 2018; 25:754-758. [PMID: 30347481 PMCID: PMC6391941 DOI: 10.1002/chem.201805215] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Indexed: 12/31/2022]
Abstract
The strain‐promoted alkyne‐azide cycloaddition (SPAAC) is the most commonly employed bioorthogonal reaction with applications in a broad range of fields. Over the years, several different cyclooctyne derivatives have been developed and investigated in regard to their reactivity in SPAAC reactions with azides. However, only a few studies examined the influence of structurally diverse azides on reaction kinetics. Herein, we report our investigations of the reactivity of primary, secondary, and tertiary azides with the cyclooctynes BCN and ADIBO applying experimental and computational methods. All azides show similar reaction rates with the sterically non‐demanding cyclooctyne BCN. However, due to the increased steric demand of the dibenzocyclooctyne ADIBO, the reactivity of tertiary azides drops by several orders of magnitude in comparison to primary and secondary azides. We show that this chemoselective behavior of tertiary azides can be exploited to achieve semiorthogonal dual‐labeling without the need for any catalyst using SPAAC exclusively.
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Affiliation(s)
- Dennis Svatunek
- Institute of Applied Synthetic Chemistry, TU Wien (Vienna University of Technology), Getreidemarkt 9/163, 1060, Vienna, Austria.,Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - Nicole Houszka
- Institute of Applied Synthetic Chemistry, TU Wien (Vienna University of Technology), Getreidemarkt 9/163, 1060, Vienna, Austria
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for, Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081, HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien (Vienna University of Technology), Getreidemarkt 9/163, 1060, Vienna, Austria
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