1
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Miura K, Nakamura H. Development of carbonic anhydrase IX-targeting molecular-targeted photodynamic therapy. Bioorg Med Chem Lett 2024; 109:129821. [PMID: 38810709 DOI: 10.1016/j.bmcl.2024.129821] [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: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024]
Abstract
The efficacy of molecular-targeted photodynamic therapy (MT-PDT) targeting carbonic anhydrase (CA) IX, a cancer-specific molecule, was demonstrated. CA ligand-directed photosensitizers 1-3 were evaluated for their ability to deactivate CAIX protein in cells. Compounds 2 and 3 selectively deactivated CAIX protein under 540 nm light without affecting internal standard proteins. Mechanistic studies revealed that compound 3 not only induced CAIX-selective light inactivation via singlet oxygen but also induced cell membrane damage, resulting in an anti-tumor effect. In vivo studies of CAIX-targeting MT-PDT revealed that treatment with compound 3 followed by light irradiation exhibited remarkable anti-tumor activity, leading to tumor degeneration and necrosis.
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Affiliation(s)
- Kazuki Miura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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2
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Chatterjee J, Bandyopadhyay A, Pattabiraman M, Sarkar R. Discovery and development of tyrosine-click (Y-click) reaction for the site-selective labelling of proteins. Chem Commun (Camb) 2024. [PMID: 38913168 DOI: 10.1039/d4cc01997k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
With the versatile utility of bio-conjugated peptides and proteins in the fields of agriculture, food, cosmetics and pharmaceutical industry, the design of smart protocols to conjugate and modulate biomolecules becomes highly desirable. During this process, the most important consideration for biochemists is the retention of configurational integrity of the biomolecules. Moreover, this type of bioconjugation of peptide and protein becomes frivolous if the reaction is not performed with precise amino acid residues. Hence, chemo-selective, as well as site-selective reactions, that are biocompatible and possess an appropriate level of reactivity are necessary. Based on click chemistry, there are so many tyrosine (Y) conjugation strategies, such as sulfur-fluoride exchange (SuFEx), sulfur-triazole exchange (SuTEx), coupling with π-allyl palladium complexes, diazonium salts, diazodicarboxyamide-based reagents etc. Among these techniques, diazodicarboxyamide-based Y-conjugation, which is commonly known as the "tyrosine-click (Y-click) reaction", has met the expectations of synthetic and biochemists for the tyrosine-specific functionalization of biomolecules. Over the past one and a half decades, significant progress has been made in the classical organic synthesis approach, as well as its biochemical, photochemical, and electrochemical variants. Despite such progress and increasing importance, the Y-click reaction has not been reviewed to document variations in its methodology, applications, and broad utility. The present article aims to provide a summary of the approaches for the modulation of biomolecules at the hotspot of tyrosine residue by employing the Y-click reaction. The article also highlights its application for the mapping of proteins, imaging of living cells, and in the fields of analytical and medicinal chemistry.
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Affiliation(s)
| | - Ayan Bandyopadhyay
- Department of Chemistry, Chapra Government College, Nadia-741123, West Bengal, India
- Department of Higher Education, Government of West Bengal, India.
| | | | - Rajib Sarkar
- Department of Higher Education, Government of West Bengal, India.
- Department of Chemistry, Muragachha Government College, Nadia-741154, West Bengal, India
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3
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Knutson SD, Buksh BF, Huth SW, Morgan DC, MacMillan DWC. Current advances in photocatalytic proximity labeling. Cell Chem Biol 2024; 31:1145-1161. [PMID: 38663396 PMCID: PMC11193652 DOI: 10.1016/j.chembiol.2024.03.012] [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: 12/20/2023] [Revised: 01/31/2024] [Accepted: 03/29/2024] [Indexed: 06/23/2024]
Abstract
Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.
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Affiliation(s)
- Steve D Knutson
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Benito F Buksh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Sean W Huth
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Danielle C Morgan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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4
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Zeng W, Xue J, Geng H, Liu X, Yang J, Shen W, Yuan Y, Qiang Y, Zhu Q. Research progress on chemical modifications of tyrosine residues in peptides and proteins. Biotechnol Bioeng 2024; 121:799-822. [PMID: 38079153 DOI: 10.1002/bit.28622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/11/2023] [Accepted: 11/26/2023] [Indexed: 02/20/2024]
Abstract
The chemical modifications (CMs) of protein is an important technique in chemical biology, protein-based therapy, and material science. In recent years, there has been rapid advances in the development of CMs of peptides and proteins, providing new approaches for peptide and protein functionalization, as well as drug discovery. In this review, we highlight the methods for chemically modifying tyrosine (Tyr) residues in different regions, offering a comprehensive exposition of the research content related to Tyr modification. This review summarizes and provides an outlook on Tyr residue modification, aiming to offer readers assistance in the site-selective modification of macromolecules and to facilitate application research in this field.
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Affiliation(s)
- Wei Zeng
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jianyuan Xue
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Haoxing Geng
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xia Liu
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jin Yang
- Department of Biotechnology and the Quality Management, Zhejiang Pharmaceutical Industry Co. Ltd., Hangzhou, China
| | - Wei Shen
- Department of Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yuqing Yuan
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yujie Qiang
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qing Zhu
- Department of Biotechnology and the Quality Management, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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5
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [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: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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6
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Huth SW, Oakley JV, Seath CP, Geri JB, Trowbridge AD, Parker DL, Rodriguez-Rivera FP, Schwaid AG, Ramil C, Ryu KA, White CH, Fadeyi OO, Oslund RC, MacMillan DWC. μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping. J Am Chem Soc 2023; 145:16289-16296. [PMID: 37471577 PMCID: PMC10809032 DOI: 10.1021/jacs.3c03325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discovery, but in many cases structural characterization is challenging or impossible. PAL has also enabled binding site mapping with peptide- and amino-acid-level resolution; however, the stoichiometric activation mode can lead to poor signal and coverage of the resident binding pocket. Additionally, each PAL probe can have its own fragmentation pattern, complicating the analysis by mass spectrometry. Here, we establish a robust and general photocatalytic approach toward the mapping of protein binding sites, which we define as identification of residues proximal to the ligand binding pocket. By utilizing a catalytic mode of activation, we obtain sets of labeled amino acids in the proximity of the target protein binding site. We use this methodology to map, in vitro, the binding sites of six protein targets, including several kinases and molecular glue targets, and furthermore to investigate the binding site of the STAT3 inhibitor MM-206, a ligand with no known crystal structure. Finally, we demonstrate the successful mapping of drug binding sites in live cells. These results establish μMap as a powerful method for the generation of amino-acid- and peptide-level target engagement data.
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Affiliation(s)
- Sean W. Huth
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - James V. Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jacob B. Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Aaron D. Trowbridge
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Adam G. Schwaid
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Carlo Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Cory H. White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Olugbeminiyi O. Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Rob C. Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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7
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Ahmad MG, Balamurali MM, Chanda K. Click-derived multifunctional metal complexes for diverse applications. Chem Soc Rev 2023; 52:5051-5087. [PMID: 37431583 DOI: 10.1039/d3cs00343d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
The Click reaction that involves Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) serves as the most potent and highly dependable tool for the development of many complex architectures. It has paved the way for the synthesis of numerous drug molecules with enhanced synthetic flexibility, reliability, specificity and modularity. It is all about bringing two different molecular entities together to achieve the required molecular properties. The utilization of Click chemistry has been well demonstrated in organic synthesis, particularly in reactions that involve biocompatible precursors. In pharmaceutical research, Click chemistry is extensively utilized for drug delivery applications. The exhibited bio-compatibility and dormancy towards other biological components under cellular environments makes Click chemistry an identified boon in bio-medical research. In this review, various click-derived transition metal complexes are discussed in terms of their applications and uniqueness. The scope of this chemistry towards other streams of applied sciences is also discussed.
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Affiliation(s)
- Md Gulzar Ahmad
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
| | - M M Balamurali
- Chemistry Division, School of Advanced Sciences, Vellore Institute of Technology, Chennai campus, Chennai 600127, Tamilnadu, India.
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore 632014, Tamilnadu, India.
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8
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Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [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: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
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Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
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9
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Qiu S, Li W, Deng T, Bi A, Yang Y, Jiang X, Li JP. Ru(bpy) 3 2+ -Enabled Cell-Surface Photocatalytic Proximity Labeling toward More Efficient Capture of Physically Interacting Cells. Angew Chem Int Ed Engl 2023; 62:e202303014. [PMID: 37165969 DOI: 10.1002/anie.202303014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023]
Abstract
Intercellular proximity labeling has emerged as a promising approach to enable the study of cell-cell interactions (CCIs), but the efficiency of current platforms is limited. Here, we use Ru(bpy)3 2+ to construct an efficient photocatalytic proximity labeling (PPL) system on the cell surface that allows the highly discriminative CCI detection with spatiotemporal resolution. Through the mechanism study and quantitative characterization on living cells, we demonstrate that the singlet-oxygen (1 O2 ) mechanism is more efficient and specific than the single electron transfer (SET) mechanism in Ru-mediated PPL. Ru(bpy)3 2+ catalysts with different cell-anchoring moieties are prepared to facilitate the catalyst loading on primary cells. Finally, based on this system, we develop a "live" T cell receptor (TCR) multimer with TCR-T cells that could sensitively identify and discriminate cells presenting antigens of different affinity, providing a powerful tool to better understand the heterogeneity of antigen presenting cells.
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Affiliation(s)
- Shuang Qiu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Wannan Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Tao Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Angzhi Bi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Xi Jiang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, 210023, Nanjing, Jiangsu, China
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10
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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11
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Park J, Tang H, Zhang P. Differentiation of Superoxide Radical Anion and Singlet Oxygen and Their Concurrent Quantifications by Nuclear Magnetic Resonance. Anal Chem 2023; 95:5293-5299. [PMID: 36926848 DOI: 10.1021/acs.analchem.2c05312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
While there have been various techniques, assays, and commercial kits developed to measure reactive oxygen species (ROS) with varying degrees of success, there is a lack of innovative methods to differentiate and quantify them simultaneously. In this work, we demonstrate a 19F nuclear magnetic resonance (NMR)-based method to differentiate two important types of ROS, superoxide radical anion and singlet oxygen, and to quantify them concurrently. By taking advantage of the unique chemical reactivity of two fluorine-containing molecules, 4-fluoro-3-methylphenyl boronic acid and 4-fluoro-3-methylphenol, serving as 19F NMR probes, we are able to differentiate and quantify, for the first time, superoxide radical anion and singlet oxygen generated by photosensitizers (PSs) concurrently. The results reveal that relative amounts of superoxide radical anion and singlet oxygen generated by a PS under light illumination are oftentimes sensitive to the environment, such as the presence or absence of electron donors. This method provides a means to identify the type of mechanism by which a PS functions under a given condition. We envision that this relatively simple, yet robust, method would be beneficial to a broad range of ROS-pertinent studies, such as photodynamic therapy and photoredox reactions.
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Affiliation(s)
- Juhyeon Park
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Hong Tang
- Alph Technologies LLC, Cincinnati, Ohio 45243, United States
| | - Peng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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12
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Madec H, Figueiredo F, Cariou K, Roland S, Sollogoub M, Gasser G. Metal complexes for catalytic and photocatalytic reactions in living cells and organisms. Chem Sci 2023; 14:409-442. [PMID: 36741514 PMCID: PMC9848159 DOI: 10.1039/d2sc05672k] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022] Open
Abstract
The development of organometallic catalysis has greatly expanded the synthetic chemist toolbox compared to only exploiting "classical" organic chemistry. Although more widely used in organic solvents, metal-based catalysts have also emerged as efficient tools for developing organic transformations in water, thus paving the way for further development of bio-compatible reactions. However, performing metal-catalysed reactions within living cells or organisms induces additional constraints to the design of reactions and catalysts. In particular, metal complexes must exhibit good efficiency in complex aqueous media at low concentrations, good cell specificity, good cellular uptake and low toxicity. In this review, we focus on the presentation of discrete metal complexes that catalyse or photocatalyse reactions within living cells or living organisms. We describe the different reaction designs that have proved to be successful under these conditions, which involve very few metals (Ir, Pd, Ru, Pt, Cu, Au, and Fe) and range from in cellulo deprotection/decaging/activation of fluorophores, drugs, proteins and DNA to in cellulo synthesis of active molecules, and protein and organelle labelling. We also present developments in bio-compatible photo-activatable catalysts, which represent a very recent emerging area of research and some prospects in the field.
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Affiliation(s)
- Hugo Madec
- Sorbonne Université, CNRS, Institut Parisien de Chimie MoléculaireParisFrancehttp://www.ipcm.fr/-Glycochimie-Organique
| | - Francisca Figueiredo
- Chimie ParisTech, PSL Université, CNRS, Institute of Chemistry for Life and Health SciencesParis 75005Francehttp://www.gassergroup.com
| | - Kevin Cariou
- Chimie ParisTech, PSL Université, CNRS, Institute of Chemistry for Life and Health SciencesParis 75005Francehttp://www.gassergroup.com
| | - Sylvain Roland
- Sorbonne Université, CNRS, Institut Parisien de Chimie MoléculaireParisFrancehttp://www.ipcm.fr/-Glycochimie-Organique
| | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie MoléculaireParisFrancehttp://www.ipcm.fr/-Glycochimie-Organique
| | - Gilles Gasser
- Chimie ParisTech, PSL Université, CNRS, Institute of Chemistry for Life and Health SciencesParis 75005Francehttp://www.gassergroup.com
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13
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Miura K, Wen Y, Tsushima M, Nakamura H. Photodynamic Therapy by Glucose Transporter 1-Selective Light Inactivation. ACS OMEGA 2022; 7:34685-34692. [PMID: 36188330 PMCID: PMC9520747 DOI: 10.1021/acsomega.2c05042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Chromophore-assisted light inactivation (CALI) was applied to molecule-targeted photodynamic therapy (PDT). In order to identify organic photosensitizers suitable for CALI, the carbonic anhydrase II (CAII) ligand, 4-sulfamoylbenzoic acid 1, was conjugated with several photosensitizers to produce compounds 2-7, whose CALI ability was evaluated by measuring their effect on CAII enzymatic activity. Di-iodinated BODIPY (I2BODIPY) exhibited excellent CAII inactivation ability, similar to that of Ru(bpy)3. The glucose-I2BODIPY conjugate (8) was synthesized as an inactivation of glucose transporter 1 (GLUT1), a protein overexpressed in many cancer cells. Under light irradiation, 8 exhibited concentration-dependent cytotoxicity with half maximal inhibitory concentration (IC50) values of 5.49, 11.14, and 8.73 μM, against human cervical carcinoma (HeLa), human lung carcinoma (A549), and human hepatocellular carcinoma (HepG2) cell lines, respectively. The GLUT1 inhibitor phloretin suppressed the cytotoxicity induced by 8 under light irradiation in a concentration-dependent manner. Western blot analysis indicated that GLUT1 was not detected in cell lines treated with 10 μM 8 under light irradiation. Furthermore, 8 reduced the levels of epidermal growth factor receptor tyrosine kinase (EGFR), phospho-ERK (Y204), and GLUT1 without affecting ERK, α-tubulin, and PCNA protein levels, whereas talaporfin sodium, a clinically approved photosensitizer for PDT, nonspecifically reduced intracellular protein levels in HeLa cells, indicating that 8 has a GLUT1-specific inactivation ability and causes light-induced cytotoxicity by modulating the EGFR/MAPK signaling pathway.
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Affiliation(s)
- Kazuki Miura
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yijin Wen
- School
of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho,
Midori-ku, Yokohama 226-8501, Japan
| | - Michihiko Tsushima
- School
of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho,
Midori-ku, Yokohama 226-8501, Japan
| | - Hiroyuki Nakamura
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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14
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Liu S, Zhao X, Shui S, Wang B, Cui Y, Dong S, Yuwen T, Liu G. PDTAC: Targeted Photodegradation of GPX4 Triggers Ferroptosis and Potent Antitumor Immunity. J Med Chem 2022; 65:12176-12187. [PMID: 36066386 DOI: 10.1021/acs.jmedchem.2c00855] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Targeted degradation of proteins, especially those regarded as undruggable or difficult to drug, attracts wide attention to develop novel therapeutic strategies. Glutathione peroxidase 4 (GPX4), the key enzyme regulating ferroptosis, is currently a target with just covalent inhibitors. Here, we developed a targeted photolysis approach and achieved efficient degradation of GPX4. The photodegradation-targeting chimeras (PDTACs) were synthesized by conjugating a clinically approved photosensitizer (verteporfin) to noninhibitory GPX4-targeting peptides. These chimeras selectively degraded the target protein in both cell lysates and living cells upon red-light irradiation. The targeted photolysis of GPX4 resulted in dominant ferroptotic cell death in malignant cancer cells. Moreover, the dying cells resulting from the PDTACs exhibited potent immunogenicity in vitro and efficiently elicited antitumor immunity in vivo. Our approach therefore provides a novel method to induce GPX4 dysfunction based on noncovalent binding and specifically trigger immunogenic ferroptosis, which may boost the application of ferroptosis in cancer immunotherapy.
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Affiliation(s)
- Sijin Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Sufang Shui
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Biao Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yingxian Cui
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Tairan Yuwen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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15
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Oslund RC, Reyes-Robles T, White CH, Tomlinson JH, Crotty KA, Bowman EP, Chang D, Peterson VM, Li L, Frutos S, Vila-Perelló M, Vlerick D, Cromie K, Perlman DH, Ingale S, Hara SDO, Roberts LR, Piizzi G, Hett EC, Hazuda DJ, Fadeyi OO. Detection of cell-cell interactions via photocatalytic cell tagging. Nat Chem Biol 2022; 18:850-858. [PMID: 35654846 DOI: 10.1038/s41589-022-01044-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/22/2022] [Indexed: 02/07/2023]
Abstract
The growing appreciation of immune cell-cell interactions within disease environments has led to extensive efforts to develop immunotherapies. However, characterizing complex cell-cell interfaces in high resolution remains challenging. Thus, technologies leveraging therapeutic-based modalities to profile intercellular environments offer opportunities to study cell-cell interactions with molecular-level insight. We introduce photocatalytic cell tagging (PhoTag) for interrogating cell-cell interactions using single-domain antibodies (VHHs) conjugated to photoactivatable flavin-based cofactors. Following irradiation with visible light, the flavin photocatalyst generates phenoxy radical tags for targeted labeling. Using this technology, we demonstrate selective synaptic labeling across the PD-1/PD-L1 axis in antigen-presenting cell-T cell systems. In combination with multiomics single-cell sequencing, we monitored interactions between peripheral blood mononuclear cells and Raji PD-L1 B cells, revealing differences in transient interactions with specific T cell subtypes. The utility of PhoTag in capturing cell-cell interactions will enable detailed profiling of intercellular communication across different biological systems.
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Affiliation(s)
- Rob C Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
| | | | - Cory H White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Jake H Tomlinson
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Kelly A Crotty
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Edward P Bowman
- Discovery Research, Merck & Co., Inc., San Francisco, CA, USA
| | - Dan Chang
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | - Lixia Li
- Genetics and Pharmacogenomics, Merck & Co., Inc., Boston, MA, USA
| | | | | | | | | | - David H Perlman
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Sampat Ingale
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | | | - Lee R Roberts
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Grazia Piizzi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Erik C Hett
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA
| | - Daria J Hazuda
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA.,Infectious Diseases and Vaccine Research, Merck & Co., Inc., West Point, PA, USA
| | - Olugbeminiyi O Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, USA. .,InduPro, Cambridge, MA, USA.
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16
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Tsushima M, Sato S, Miura K, Niwa T, Taguchi H, Nakamura H. Intracellular photocatalytic-proximity labeling for profiling protein-protein interactions in microenvironments. Chem Commun (Camb) 2022; 58:1926-1929. [PMID: 35040832 DOI: 10.1039/d1cc05764b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intracellular photocatalytic-proximity labeling (iPPL) was developed to profile protein-protein interactions in the microenvironment of living cells. Acriflavine was found to be an efficient cell-membrane-permeable photocatalyst for introduction into the genetically HaloTag-fused protein of interest for iPPL with a radical labeling reagent, 1-methyl-4-arylurazole. iPPL was applied to the histone-associated protein H2B in HaloTag-H2B expressing HEK293FT cells. The proteins directly interacting with histones and RNA-binding proteins were selectively labeled in the intracellular environment, suggesting that the iPPL method has a smaller labeling radius (CA. 6 nm) than the BioID and APEX methods.
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Affiliation(s)
- Michihiko Tsushima
- School of Life Science and Engineering, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Shinichi Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Kazuki Miura
- School of Life Science and Engineering, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
| | - Tatsuya Niwa
- School of Life Science and Engineering, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hideki Taguchi
- School of Life Science and Engineering, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Hiroyuki Nakamura
- School of Life Science and Engineering, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
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17
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Sato S. Protein Chemical Modification Using Highly Reactive Species and Spatial Control of Catalytic Reactions. Chem Pharm Bull (Tokyo) 2022; 70:95-105. [PMID: 35110442 DOI: 10.1248/cpb.c21-00915] [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] [Indexed: 12/20/2022]
Abstract
Protein bioconjugation has become an increasingly important research method for introducing artificial functions in to protein with various applications, including therapeutics and biomaterials. Due to its amphiphilic nature, only a few tyrosine residues are exposed on the protein surface. Therefore, tyrosine residue has attracted attention as suitable targets for site-specific modification, and it is the most studied amino acid residue for modification reactions other than lysine and cysteine residues. In this review, we present the progress of our tyrosine chemical modification studies over the past decade. We have developed several different catalytic approaches to selectively modify tyrosine residues using peroxidase, laccase, hemin, and ruthenium photocatalysts. In addition to modifying tyrosine residues by generating radical species through single-electron transfer, we have developed a histidine modification method that utilizes singlet oxygen generated by photosensitizers. These highly reactive chemical species selectively modify proteins in close proximity to the enzyme/catalyst. Taking advantage of the spatially controllable reaction fields, we have developed novel methods for site-specific antibody modification, detecting hotspots of oxidative stress, and target identification of bioactive molecules.
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Affiliation(s)
- Shinichi Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University
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18
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Taylor MT. Photochemical protein modification in complex biological environments: recent advances and considerations for future chemical methods development. Biol Chem 2022; 403:413-420. [PMID: 35073619 PMCID: PMC10163948 DOI: 10.1515/hsz-2021-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/12/2022] [Indexed: 12/29/2022]
Abstract
Abstract
The development of organic reactions that covalently modify biological matter in complex biological mixtures has become an invaluable asset in drug discovery. Out of the techniques developed to date, optically controlled chemistries are of particular utility owing to both the spatiotemporal control afforded by optical control as well as the impressive array of transformations that are driven by the highly reactive intermediates generated upon excitation. This minireview discusses recent advances in the development of photochemical reactions for use in complex mixtures and highlights key considerations for future photochemical reaction designs.
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Affiliation(s)
- Michael T Taylor
- Department of Chemistry, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA
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19
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Liu W, Watson EE, Winssinger N. Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
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20
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Abstract
A laccase-catalysed tyrosine click reaction proceeded between the tyrosine modification reagent N-methyl luminol and tyrosine residues in peptides/proteins. Laccase-catalysed tyrosine-specific modification under mild reaction conditions (shaking at 37 °C) was more efficient than previously reported tyrosine click reactions using hemin, horseradish peroxidase (HRP) or electrochemistry.
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Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-13, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Keita Nakane
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-13, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. and School of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, R1-13, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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22
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Kimura H, Nagasato N, Kato N, Kojima M, Enomoto C, Nakata E, Takashima H. Photophysical and elecron-transfer reaction properties of tris(2,2’-bipyridine)ruthenium(II)-based inhibitors that covalently bound to the active site of chymotrypsin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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23
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Nakane K, Sato S, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Ishikawa M, Nakamura H. Proximity Histidine Labeling by Umpolung Strategy Using Singlet Oxygen. J Am Chem Soc 2021; 143:7726-7731. [PMID: 33904715 DOI: 10.1021/jacs.1c01626] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
While electrophilic reagents for histidine labeling have been developed, we report an umpolung strategy for histidine functionalization. A nucleophilic small molecule, 1-methyl-4-arylurazole, selectively labeled histidine under singlet oxygen (1O2) generation conditions. Rapid histidine labeling can be applied for instant protein labeling. Utilizing the short diffusion distance of 1O2 and a technique to localize the 1O2 generator, a photocatalyst in close proximity to the ligand-binding site, we demonstrated antibody Fc-selective labeling on magnetic beads functionalized with a ruthenium photocatalyst and Fc ligand, ApA. Three histidine residues located around the ApA binding site were identified as labeling sites by liquid chromatography-mass spectrometry analysis. This result suggests that 1O2-mediated histidine labeling can be applied to a proximity labeling reaction on the nanometer scale.
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Affiliation(s)
- Keita Nakane
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Shinichi Sato
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Michihiko Tsushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Shusuke Tomoshige
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Minoru Ishikawa
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
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24
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Interrogating biological systems using visible-light-powered catalysis. Nat Rev Chem 2021; 5:322-337. [PMID: 37117838 DOI: 10.1038/s41570-021-00265-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Light-powered catalysis has found broad utility as a chemical transformation strategy, with widespread impact on energy, environment, drug discovery and human health. A noteworthy application impacting human health is light-induced sensitization of cofactors for photodynamic therapy in cancer treatment. The clinical adoption of this photosensitization approach has inspired the search for other photochemical methods, such as photoredox catalysis, to influence biological discovery. Over the past decade, light-mediated catalysis has enabled the discovery of valuable synthetic transformations, propelling it to become a highly utilized chemical synthesis strategy. The reaction components required to achieve a photoredox reaction are identical to photosensitization (catalyst, light source and substrate), making it ideally suited for probing biological environments. In this Review, we discuss the therapeutic application of photosensitization and advancements made in developing next-generation catalysts. We then highlight emerging uses of photoredox catalytic methods for protein bioconjugation and probing complex cellular environments in living cells.
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25
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Seath CP, Trowbridge AD, Muir TW, MacMillan DWC. Reactive intermediates for interactome mapping. Chem Soc Rev 2021; 50:2911-2926. [PMID: 33458734 DOI: 10.1039/d0cs01366h] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interactions of biomolecules underpin all cellular processes, and the understanding of their dynamic interplay can lead to significant advances in the treatment of disease through the identification of novel therapeutic strategies. Protein-protein interactions (PPIs) in particular play a vital role within this arena, providing the basis for the majority of cellular signalling pathways. Despite their great importance, the elucidation of weak or transient PPIs that cannot be identified by immunoprecipitation remains a significant challenge, particularly in a disease relevant cellular environment. Recent approaches towards this goal have utilized the in situ generation of high energy intermediates that cross-link with neighboring proteins, providing a snapshot of the biomolecular makeup of the local area or microenvironment, termed the interactome. In this tutorial review, we discuss these reactive intermediates, how they are generated, and the impact they have had on the discovery of new biology. Broadly, we believe this strategy has the potential to significantly accelerate our understanding of PPIs and how they affect cellular physiology.
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Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA.
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26
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Guo AD, Wu KH, Chen XH. Light-induced efficient and residue-selective bioconjugation of native proteins via indazolone formation. RSC Adv 2021; 11:2235-2241. [PMID: 35424183 PMCID: PMC8693682 DOI: 10.1039/d0ra10154k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 12/03/2022] Open
Abstract
Chemical modification of proteins has emerged as a powerful tool to realize enormous applications, such as development of novel biologics and functional studies of individual protein. We report a light-induced lysine-selective native protein conjugation approach via indazolone formation, conferring reliable chemoselectivity, excellent efficiency, temporal control and biocompatibility under operationally simple and mild conditions, in vitro and in living systems. This straightforward protocol demonstrates the generality and accessibility for direct and rapid functionalization of diverse native proteins, which suggests a new avenue of great importance to bioconjugation, medicinal chemistry and chemical biology.
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Affiliation(s)
- An-Di Guo
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ke-Huan Wu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Xiao-Hua Chen
- Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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27
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Bissonnette NB, Ryu KA, Reyes‐Robles T, Wilhelm S, Tomlinson JH, Crotty KA, Hett EC, Roberts LR, Hazuda DJ, Jared Willis M, Oslund RC, Fadeyi OO. Design of a Multiuse Photoreactor To Enable Visible-Light Photocatalytic Chemical Transformations and Labeling in Live Cells. Chembiochem 2020; 21:3555-3562. [PMID: 32749732 PMCID: PMC7756335 DOI: 10.1002/cbic.202000392] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Despite the growing use of visible-light photochemistry in both chemistry and biology, no general low-heat photoreactor for use across these different disciplines exists. Herein, we describe the design and use of a standardized photoreactor for visible-light-driven activation and photocatalytic chemical transformations. Using this single benchtop photoreactor, we performed photoredox reactions across multiple visible light wavelengths, a high-throughput photocatalytic cross-coupling reaction, and in vitro labeling of proteins and live cells. Given the success of this reactor in all tested applications, we envision that this multi-use photoreactor will be widely used in biology, chemical biology, and medicinal chemistry settings.
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Affiliation(s)
- Noah B. Bissonnette
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Keun Ah Ryu
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Tamara Reyes‐Robles
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Sharon Wilhelm
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Jake H. Tomlinson
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Kelly A. Crotty
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Erik C. Hett
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Lee R. Roberts
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
| | - Daria J. Hazuda
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
- Infectious Diseases and Vaccine ResearchMerck & Co.Inc. Merck Research LaboratoriesWest PointPA 19486USA
| | | | - Rob C. Oslund
- Exploratory Science CenterMerck & Co.Inc.320 Bent StreetCambridgeMA 02141USA
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28
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van Lier RCW, de Bruijn AD, Roelfes G. A Water-Soluble Iridium Photocatalyst for Chemical Modification of Dehydroalanines in Peptides and Proteins. Chemistry 2020; 27:1430-1437. [PMID: 32896943 PMCID: PMC7898865 DOI: 10.1002/chem.202002599] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/04/2020] [Indexed: 12/27/2022]
Abstract
Dehydroalanine (Dha) residues are attractive noncanonical amino acids that occur naturally in ribosomally synthesised and post-translationally modified peptides (RiPPs). Dha residues are attractive targets for selective late-stage modification of these complex biomolecules. In this work, we show the selective photocatalytic modification of dehydroalanine residues in the antimicrobial peptide nisin and in the proteins small ubiquitin-like modifier (SUMO) and superfolder green fluorescent protein (sfGFP). For this purpose, a new water-soluble iridium(III) photoredox catalyst was used. The design and synthesis of this new photocatalyst, [Ir(dF(CF3 )ppy)2 (dNMe3 bpy)]Cl3 , is presented. In contrast to commonly used iridium photocatalysts, this complex is highly water soluble and allows peptides and proteins to be modified in water and aqueous solvents under physiologically relevant conditions, with short reaction times and with low reagent and catalyst loadings. This work suggests that photoredox catalysis using this newly designed catalyst is a promising strategy to modify dehydroalanine-containing natural products and thus could have great potential for novel bioconjugation strategies.
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Affiliation(s)
- Roos C W van Lier
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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29
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Dai SY, Yang D. A Visible and Near-Infrared Light Activatable Diazocoumarin Probe for Fluorogenic Protein Labeling in Living Cells. J Am Chem Soc 2020; 142:17156-17166. [PMID: 32870680 DOI: 10.1021/jacs.0c08068] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical modification of proteins in living cells permits valuable glimpses into the molecular interactions that underpin dynamic cellular events. While genetic engineering methods are often preferred, selective labeling of endogenous proteins in a complex intracellular milieu with chemical approaches represents a significant challenge. In this study, we report novel diazocoumarin compounds that can be photoactivated by visible (430-490 nm) and near-infrared light (800 nm) irradiation to photo-uncage reactive carbene intermediates, which could subsequently undergo an insertion reaction with concomitant fluorescence "turned on". With these new molecules in hand, we have developed a new approach for rapid, selective, and fluorogenic labeling of endogenous protein in living cells. By using CA-II and eDHFR as model proteins, we demonstrated that subcellular localization of proteins can be precisely visualized by live-cell imaging and protein levels can be reliably quantified in multiple cell types using flow cytometry. Dynamic protein regulations such as hypoxia-induced CA-IX accumulation can also be detected. In addition, by two-photon excitation with an 800 nm laser, cell-selective labeling can also be achieved with spatially controlled irradiation. Our method circumvents the cytotoxicity of UV light and obviates the need for introducing external reporters with "click chemistries". We believe that this approach of fluorescence labeling of endogenous protein by bioorthogonal photoirradiation opens up exciting opportunities for discoveries and mechanistic interrogation in chemical biology.
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Affiliation(s)
- Sheng-Yao Dai
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dan Yang
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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30
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Tsushima M, Sato S, Nakane K, Nakamura H. Target Protein Identification on Photocatalyst-Functionalized Magnetic Affinity Beads. ACTA ACUST UNITED AC 2020; 101:e108. [PMID: 32603537 DOI: 10.1002/cpps.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Although various affinity chromatography and photoaffinity labeling methods have been developed for target protein identification of bioactive molecules, it is often difficult to detect proteins that bind the ligand with weak transient affinity using these techniques. We have developed single electron transfer-mediated tyrosine labeling using ruthenium photocatalysts. Proximity labeling using 1-methyl-4-aryl-urazole (MAUra) labels proteins in close proximity to the photocatalyst with high efficiency and selectivity. Performing this labeling reaction on affinity beads makes it possible to label proteins that bind the ligand with weak transient affinity. In this article, novel protocols are described for target protein identification using photocatalyst proximity labeling on ruthenium photocatalyst-functionalized magnetic affinity beads. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of ruthenium photocatalyst Basic Protocol 2: Synthesis of azide- or desthiobiotin-conjugated labeling reagents Basic Protocol 3: Preparation of photocatalyst and ligand-functionalized affinity beads Basic Protocol 4: Target protein labeling in cell lysate Basic Protocol 5: Enrichment of labeled proteins with MAUra-DTB for LC-MS/MS analysis Basic Protocol 6: 2D-DIGE analysis of fluorescence-labeled proteins.
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Affiliation(s)
- Michihiko Tsushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan
| | - Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan
| | - Keita Nakane
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, Japan
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31
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Beard HA, Hauser JR, Walko M, George RM, Wilson AJ, Bon RS. Photocatalytic proximity labelling of MCL-1 by a BH3 ligand. Commun Chem 2019; 2:133. [PMID: 33763603 PMCID: PMC7610391 DOI: 10.1038/s42004-019-0235-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Ligand-directed protein labelling allows the introduction of diverse chemical functionalities onto proteins without the need for genetically encoded tags. Here we report a method for the rapid labelling of a protein using a ruthenium-bipyridyl (Ru(II)(bpy)3)-modified peptide designed to mimic an interacting BH3 ligand within a BCL-2 family protein-protein interactions. Using sub-stoichiometric quantities of (Ru(II)(bpy)3)-modified NOXA-B and irradiation with visible light for 1 min, the anti-apoptotic protein MCL-1 can be photolabelled with a variety of functional tags. In contrast with previous reports on Ru(II)(bpy)3-mediated photolabelling, tandem mass spectrometry experiments reveal that the labelling site is a cysteine residue of MCL-1. MCL-1 can be labelled selectively in mixtures with other proteins, including the structurally related BCL-2 member, BCL-xL. These results demonstrate that proximity-induced photolabelling is applicable to interfaces that mediate protein-protein interactions, and pave the way towards future use of ligand-directed proximity labelling for dynamic analysis of the interactome of BCL-2 family proteins.
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Affiliation(s)
- Hester A Beard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Jacob R Hauser
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Martin Walko
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Rachel M George
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Robin S Bon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.,Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT laboratories, University of Leeds, Leeds LS2 9JT, UK
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32
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Abstract
The chemical labeling of proteins with synthetic small compounds is a key technique in chemical biology, protein-based therapy, and material science. Much of the chemical labeling of native proteins, however, depends on the labeling of lysine and cysteine residues. While those methods have contributed significantly to native protein labeling, alternative methods that can modify different amino acid residues are still required. Here we report the development of a novel methodology of oxidative tyrosine labeling, which was inspired by the single-electron transfer reaction in biological systems. The tyrosine labeling methods were developed using small compounds such as N-methyl luminol derivative, N'-acyl-N,N-phenylenediamine, and 1-methyl-4-aryl-urazole under labeling conditions using a hemin, peroxidase, or ruthenium photocatalyst. These methods were applied to target- and site-selective protein modification.
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Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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33
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Protein Chemical Labeling Using Biomimetic Radical Chemistry. Molecules 2019; 24:molecules24213980. [PMID: 31684188 PMCID: PMC6864698 DOI: 10.3390/molecules24213980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 01/17/2023] Open
Abstract
Chemical labeling of proteins with synthetic low-molecular-weight probes is an important technique in chemical biology. To achieve this, it is necessary to use chemical reactions that proceed rapidly under physiological conditions (i.e., aqueous solvent, pH, low concentration, and low temperature) so that protein denaturation does not occur. The radical reaction satisfies such demands of protein labeling, and protein labeling using the biomimetic radical reaction has recently attracted attention. The biomimetic radical reaction enables selective labeling of the C-terminus, tyrosine, and tryptophan, which is difficult to achieve with conventional electrophilic protein labeling. In addition, as the radical reaction proceeds selectively in close proximity to the catalyst, it can be applied to the analysis of protein–protein interactions. In this review, recent trends in protein labeling using biomimetic radical reactions are discussed.
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34
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35
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Sato S, Tsushima M, Nakamura H. Utilization of Single Electron Transfer Reaction in Protein Chemical Labeling. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | | | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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36
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Ohata J, Martin SC, Ball ZT. Metallvermittelte Funktionalisierung natürlicher Peptide und Proteine: Biokonjugation mit Übergangsmetallen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807536] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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37
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Ohata J, Martin SC, Ball ZT. Metal‐Mediated Functionalization of Natural Peptides and Proteins: Panning for Bioconjugation Gold. Angew Chem Int Ed Engl 2019; 58:6176-6199. [DOI: 10.1002/anie.201807536] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jun Ohata
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Samuel C. Martin
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
| | - Zachary T. Ball
- Department of Chemistry Rice University 6100 Main Houston TX 77005 USA
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38
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Sato S, Yoshida M, Hatano K, Matsumura M, Nakamura H. N’-acyl-N-methylphenylenediamine as a novel proximity labeling agent for signal amplification in immunohistochemistry. Bioorg Med Chem 2019; 27:1110-1118. [DOI: 10.1016/j.bmc.2019.01.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/22/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
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39
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Angerani S, Winssinger N. Visible Light Photoredox Catalysis Using Ruthenium Complexes in Chemical Biology. Chemistry 2019; 25:6661-6672. [PMID: 30689234 DOI: 10.1002/chem.201806024] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/24/2022]
Abstract
The development of bioorthogonal reactions have had a transformative impact in chemical biology and the quest to expand this toolbox continues. Herein we review recent applications of ruthenium-catalyzed photoredox reactions used in chemical biology.
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Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
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40
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Tsushima M, Sato S, Niwa T, Taguchi H, Nakamura H. Catalyst-proximity protein chemical labelling on affinity beads targeting endogenous lectins. Chem Commun (Camb) 2019; 55:13275-13278. [DOI: 10.1039/c9cc05231c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Catalyst-proximity labelling on affinity beads enables the identification of ligand-binding proteins such as lectins, which cannot be analyzed by conventional techniques. 1-Methyl-4-arylurazole (MAUra) efficiently labels proteins bound to the beads.
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Affiliation(s)
- Michihiko Tsushima
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Shinichi Sato
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tatsuya Niwa
- Cell Biology Center
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hideki Taguchi
- Cell Biology Center
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
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41
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Tamura T, Hamachi I. Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems. J Am Chem Soc 2018; 141:2782-2799. [DOI: 10.1021/jacs.8b11747] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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42
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Bottecchia C, Noël T. Photocatalytic Modification of Amino Acids, Peptides, and Proteins. Chemistry 2018; 25:26-42. [PMID: 30063101 PMCID: PMC6348373 DOI: 10.1002/chem.201803074] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/27/2018] [Indexed: 02/06/2023]
Abstract
In the last decade, visible‐light photoredox catalysis has emerged as a powerful strategy to enable novel transformations in organic synthesis. Owing to mild reaction conditions (i.e., room temperature, use of visible light) and high functional‐group tolerance, photoredox catalysis could represent an ideal strategy for chemoselective biomolecule modification. Indeed, a recent trend in photoredox catalysis is its application to the development of novel methodologies for amino acid modification. Herein, an up‐to‐date overview of photocatalytic methodologies for the modification of single amino acids, peptides, and proteins is provided. The advantages offered by photoredox catalysis and its suitability in the development of novel biocompatible methodologies are described. In addition, a brief consideration of the current limitations of photocatalytic approaches, as well as future challenges to be addressed, are discussed.
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Affiliation(s)
- Cecilia Bottecchia
- Department of Chemical Engineering and Chemistry, Micro Flow Chemistry and Process Technology, Eindhoven University of Technology, De Rondom 70 (STO 1.37), 5612 AP, Eindhoven, The Netherlands
| | - Timothy Noël
- Department of Chemical Engineering and Chemistry, Micro Flow Chemistry and Process Technology, Eindhoven University of Technology, De Rondom 70 (STO 1.37), 5612 AP, Eindhoven, The Netherlands
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43
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Connell TU, Donnelly PS. Labelling proteins and peptides with phosphorescent d6 transition metal complexes. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2017.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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45
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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46
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Sato S, Tsushima M, Nakamura K, Nakamura H. [Development and Application of Catalytic Tyrosine Modification]. YAKUGAKU ZASSHI 2018; 138:39-46. [PMID: 29311464 DOI: 10.1248/yakushi.17-00186-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chemical labeling of proteins with synthetic probes is a key technique used in chemical biology, protein-based therapy, and material science. Much of the chemical labeling of native proteins, however, depends on the labeling of lysine and cysteine residues. While those methods have significantly contributed to native protein labeling, alternative methods that can modify different amino acid residues are still required. Herein we report the development of a novel methodology of tyrosine labeling, inspired by the luminol chemiluminescence reaction. Tyrosine residues are often exposed on a protein's surface and are thus expected to be good targets for protein functionalization. In our studies so far, we have found that 1) hemin oxidatively activates luminol derivatives as a catalyst, 2) N-methyl luminol derivative specifically forms a covalent bond with a tyrosine residue among the 20 kinds of natural amino acid residues, and 3) the efficiency of tyrosine labeling with N-methyl luminol derivative is markedly improved by using horseradish peroxidase (HRP) as a catalyst. We were able to use molecular oxygen as an oxidant under HRP/NADH conditions. By using these methods, the functionalization of purified proteins was carried out. Because N-methyl luminol derivative is an excellent protein labeling reagent that responds to the activation of peroxidase, this new method is expected to open doors to such biological applications as the signal amplification of HRP-conjugated antibodies and the detection of protein association in combination with peroxidase-tag technology.
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Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Michihiko Tsushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Kosuke Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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47
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Sato S, Tsushima M, Nakamura H. Target-protein-selective inactivation and labelling using an oxidative catalyst. Org Biomol Chem 2018; 16:6168-6179. [DOI: 10.1039/c8ob01484a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reactive oxygen species (ROS) and radical species generated by oxidative single-electron transfer (SET) catalysts induce local environmental oxidative reactions, resulting in protein inactivation and labelling in proximity to the catalysts.
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Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Michihiko Tsushima
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
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48
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Sato S, Hatano K, Tsushima M, Nakamura H. 1-Methyl-4-aryl-urazole (MAUra) labels tyrosine in proximity to ruthenium photocatalysts. Chem Commun (Camb) 2018; 54:5871-5874. [DOI: 10.1039/c8cc02891e] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The 1-methyl-4-aryl-urazole (MAUra) structure was found to be a novel tyrosyl radical trapping agent to label tyrosine residues effectively in proximity to ruthenium photocatalysts.
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Affiliation(s)
- Shinichi Sato
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kensuke Hatano
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Michihiko Tsushima
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science
- Institute of Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
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49
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Tamura T, Song Z, Amaike K, Lee S, Yin S, Kiyonaka S, Hamachi I. Affinity-Guided Oxime Chemistry for Selective Protein Acylation in Live Tissue Systems. J Am Chem Soc 2017; 139:14181-14191. [DOI: 10.1021/jacs.7b07339] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Zhining Song
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shin Lee
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sifei Yin
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, United Kingdom
| | - Shigeki Kiyonaka
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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Abreu FD, Paulo TDF, Gehlen MH, Ando RA, Lopes LGF, Gondim ACS, Vasconcelos MA, Teixeira EH, Sousa EHS, de Carvalho IMM. Aryl-Substituted Ruthenium(II) Complexes: A Strategy for Enhanced Photocleavage and Efficient DNA Binding. Inorg Chem 2017; 56:9084-9096. [DOI: 10.1021/acs.inorgchem.7b01108] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Felipe Diógenes Abreu
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
| | - Tercio de F. Paulo
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
| | - Marcelo H. Gehlen
- Instituto de Química de São
Carlos, Universidade de São Paulo, 13566-590 São
Carlos, São Paulo, Brazil
| | - Rômulo A. Ando
- Instituto
de Química, Universidade de São Paulo, Cx. Postal 26077, 05508-000 São Paulo, Brazil
| | - Luiz G. F. Lopes
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
| | - Ana Cláudia S. Gondim
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
| | - Mayron A. Vasconcelos
- Laboratório Integrado de Biomoléculas, Departamento
de Patologia e Medicina Legal, Universidade Federal do Ceará, 60441−750 Fortaleza, Ceará Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências
Exatas e Naturais, Universidade do Estado do Rio Grande do Norte, 59625-620, Mossoró, Rio Grande do Norte, Brazil
| | - Edson H. Teixeira
- Laboratório Integrado de Biomoléculas, Departamento
de Patologia e Medicina Legal, Universidade Federal do Ceará, 60441−750 Fortaleza, Ceará Brazil
| | - Eduardo Henrique Silva Sousa
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
| | - Idalina Maria Moreira de Carvalho
- Laboratório
de Bioinorgânica, Departamento de Química Orgânica
e Inorgânica, Universidade Federal do Ceará, Cx. Postal 6021, 60440-900 Fortaleza, Ceará Brazil
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