1
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Guo SL, Xiao YH, Pan BB, Su XC. Site-Specific Anchoring a Luminescent Tag in a Protein with Non-Emissive Iridium(III) Complex. Chembiochem 2024; 25:e202300798. [PMID: 38169080 DOI: 10.1002/cbic.202300798] [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: 11/24/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 01/05/2024]
Abstract
Site-specific modification of proteins with synthetic fluorescent tag effectively improves the resolution of imaging, and such a labeling method with negligible three-dimensional structural perturbations and minimal impact on the biological functions of proteins is of high interest to dissect the high-resolution activities of biomolecules in complex systems. To this end, several non-emissive iridium(III) complexes [Ir(C-N)2 (H2 O)2 ]+ OTF- (C-N denotes various cyclometalated ligands) were designed and synthesized. These complexes were tested for attaching a protein by coordinating to H/X (HisMet, HisHis, and HisCys) that are separated by i and i+4 in α-helix. Replacement of the two labile water ligands in the iridium(III) complex by a protein HisHis pair increases the luminescent intensity up to over 100 folds. This labeling approach has been demonstrated in a highly specific and efficient manner in a number of proteins, and it is also feasible for labeling target proteins in cell lysates.
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Affiliation(s)
- Shu-Li Guo
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu-Hao Xiao
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin-Bin Pan
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
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2
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Shigenaga A, Kyan R. Theoretical study to gain fundamental insight into reaction mechanism of N-S acyl transfer of N-sulfanylethylanilide-based protein labeling reagent on protein surface. J Pept Sci 2023; 29:e3526. [PMID: 37257834 DOI: 10.1002/psc.3526] [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: 04/10/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/02/2023]
Abstract
Elucidation of protein function is one of the central issues in the field of life sciences. To study the function of proteins not in isolation, but in a cell or its lysate, thus, it is necessary to selectively label the target protein in a mixture. Affinity labeling is one of several widely used methods for selective labeling; however, this method has the disadvantage that the labeling reagent is always activated, albeit weakly. Therefore, fine-tuning of the reactivity and/or reaction conditions is generally required for successful target-selective labeling. We previously developed a new affinity labeling reagent with N-sulfanylethylanilide (SEAlide) as a key reactive unit. It was designed based on the following hypotheses. SEAlide is less reactive and does not label in the absence of a target protein. Upon target binding, amino acid side-chain functional groups on the target surface convert SEAlide into a thioester form via N-S acyl transfer, allowing the target to be labeled. However, no evidence has been obtained so far to directly prove the hypothesis. In this study, we examine whether amino acid side-chain functional groups can activate SEAlide from the viewpoint of theoretical chemistry. The theoretical studies show that the activation free energy and enthalpy of the acyl transfer of SEAlide are reduced in the presence of methylammonium, which is a model for the protonated side chain of Lys, and acetate, which is a model for the deprotonated side chain of Asp/Glu. It suggests that Lys and Asp/Glu side chains could potentially stabilize the activation transition states to accelerate the thioester formation. Furthermore, the significant decrease in the activation enthalpy indicates that the contribution of entropy to the transition state is large. This result supports the original hypothesis that the SEAlide-based labeling reagent is efficiently activated by binding to the target protein.
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Affiliation(s)
- Akira Shigenaga
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Japan
| | - Ryuji Kyan
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Japan
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3
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Thimaradka V, Utsunomiya H, Tamura T, Hamachi I. Endogenous Cell-Surface Receptor Modification by Metal Chelation-Assisted Pyridinium Oxime Catalyst. Org Lett 2023; 25:2118-2122. [PMID: 36947590 DOI: 10.1021/acs.orglett.3c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Organocatalyst-mediated acyl transfer reactions hold promise for selective protein labeling in biological milieu. However, they often suffer from off-target reactions and high background signals because of the requirement of high concentrations of substrates. Here, we report a new catalytic protein acylation strategy promoted by the His-tag/NiNTA interaction. The recognition-assisted activation mechanism allows efficient protein labeling even with >10-fold lower substrate concentrations than conventional reactions, thereby enabling highly selective and efficient cell-surface receptor modification in live cells.
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Affiliation(s)
- Vikram Thimaradka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hayata Utsunomiya
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- 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
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyodaku, Tokyo 102-0075, Japan
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4
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Sakamoto S, Hamachi I. Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
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5
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Liu Z, Li B, Song L, Zhang H. Pillar[ n]arene-calix[ m]arene hybrid macrocyclic structures. RSC Adv 2022; 12:28185-28195. [PMID: 36320255 PMCID: PMC9528731 DOI: 10.1039/d2ra05118d] [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: 08/16/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023] Open
Abstract
To reserve planar chirality, enhance molecular recognition, and build advanced self-assemblies, hybrid macrocyclic hosts containing rigid pillar[n]arene and flexible calix[m]arene were designed, prepared and investigated for interesting applications. This review summarizes and discusses different synthetic strategies for constructing hybrid macrocyclic structures. Pillar[n]arene dimer with rigid aromatic double bridges provided the possibility of introducing calix[m]arene cavities, where the planar chirality was reserved in the structure of pillararene. The capacity for molecular recognition was enhanced by hybrid macrocyclic cavities. Interestingly, the obtained pillar[n]arene-calix[m]arene could self-assemble into "channels" and "honeycomb" in both the solid state and solution phase as well as donate the molecular architecture as the wheel for the formation of mechanically interlocked molecules, such as rotaxane. In addition, the pillar[n]arene and calix[m]arene could also be coupled together to produce pillar[n]arene embeded 1,3-alternate and cone conformational calix[m]arene derivatives, which could catalyze the oxidative polymerization of aniline in aqueous solutions. Except for building hybrid cyclophanes by covalent bonds, weak supramolecular interactions were used to prepare pillar[n]arene-calix[m]arene analogous composites with other pillar-like pillar[n]pyridiniums and calix-like calix[m]pyrroles, exhibiting reasonable performances in enhancing molecular recognition and trapping solvent molecules.
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Affiliation(s)
- Zhaona Liu
- Medical School, Xi'an Peihua University Xi'an 710125 Shaanxi China
| | - Bing Li
- School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an Shaanxi 710049 China
| | - Leqian Song
- School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an Shaanxi 710049 China
| | - Huacheng Zhang
- School of Chemical Engineering and Technology, Xi'an Jiaotong University Xi'an Shaanxi 710049 China
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6
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A bifunctional vinyl-sulfonium tethered peptide induced by thio-Michael-type addition reaction. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Nakane K, Niwa T, Tsushima M, Tomoshige S, Taguchi H, Nakamura H, Ishikawa M, Sato S. BODIPY Catalyzes Proximity‐Dependent Histidine Labelling. ChemCatChem 2022. [DOI: 10.1002/cctc.202200077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Keita Nakane
- Tohoku University: Tohoku Daigaku Graduate School of Life Science JAPAN
| | - Tatsuya Niwa
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Cell Biology Center, Institute of Innovative research JAPAN
| | - Michihiko Tsushima
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Laboratory for Chemistry and Life Science, Institute of Innovative Research JAPAN
| | - Shusuke Tomoshige
- Tohoku University: Tohoku Daigaku Graduate School of Life Sciences JAPAN
| | - Hideki Taguchi
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Cell Biology Center, Institute of Innovative Research JAPAN
| | - Hiroyuki Nakamura
- Tokyo Institute of Technology: Tokyo Kogyo Daigaku Laboratory for Chemistry and Life Science, Institute of Innovative Research JAPAN
| | - Minoru Ishikawa
- Tohoku University: Tohoku Daigaku Graduate School of Life Sciences JAPAN
| | - Shinichi Sato
- Tohoku University: Tohoku Daigaku Frontier Research Institute for Interdisciplinary Sciences 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577 Miyagi JAPAN
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8
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Wan C, Feng Y, Hou Z, Lian C, Zhang L, An Y, Sun J, Yang D, Jiang C, Yin F, Wang R, Li Z. Electrophilic Sulfonium-Promoted Peptide and Protein Amidation in Aqueous Media. Org Lett 2021; 24:581-586. [PMID: 34968069 DOI: 10.1021/acs.orglett.1c04017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel amidation strategy using electrophilic sulfonium, which is soluble and stable in aqueous conditions, was developed. The sulfoniums could activate thioacid and carboxyl acid to efficiently react with amines to afford amides. This method enables applications in amidation in both aqueous media and solid-phase peptide synthesis, peptide/protein modifications, and reactive lysines of a proteome at pH 10 with activity-based protein profiling. A peptide ligand-directed labeling of the USP7-UBL2 domain was also performed using this method.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Yuan Feng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China.,Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Jinming Sun
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, P. R. China
| | - Chenran Jiang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
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9
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Zhang Z, Nakata E, Dinh H, Saimura M, Rajendran A, Matsuda K, Morii T. Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation. Chemistry 2021; 27:18118-18128. [PMID: 34747070 DOI: 10.1002/chem.202103304] [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] [Received: 09/11/2021] [Indexed: 11/09/2022]
Abstract
Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.
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Affiliation(s)
- Zhengxiao Zhang
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Masayuki Saimura
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | | | - Kazunari Matsuda
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Uji, Kyoto, 6110011, Japan
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10
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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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11
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Lian C, Li Y, Hou Z, Zhong W, Tian Y, Yin F, Li Z, Zhou D, Wang R. Proximity-induced amino-yne reaction for selective MDM4 conjugation via propargylated sulfonium. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Takahashi T, Hagiwara H. Detecting ligand-protein interactions inside cells using reactive peptide tags and split luciferase. Chem Commun (Camb) 2021; 57:9906-9909. [PMID: 34494618 DOI: 10.1039/d1cc03556h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a method for detecting ligand-protein interactions occurring within cells using short peptide reactive tags appended to ligands and proteins, along with a split NanoLuc luciferase. This method can be applied to estimate the binding affinities of ligand-protein interactions and to detect the interactions of proteins with unstable synthetic ligands inside the cells.
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Affiliation(s)
- Tsuyoshi Takahashi
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
| | - Hiroaki Hagiwara
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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13
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Kumar M, Reddy NC, Rai V. Chemical technologies for precise protein bioconjugation interfacing biology and medicine. Chem Commun (Camb) 2021; 57:7083-7095. [PMID: 34180471 DOI: 10.1039/d1cc02268g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins provide an excellent means to monitor and regulate biological processes. Hence, a precise chemical toolbox for their modification becomes indispensable. In this perspective, this feature article outlines our efforts to establish the core principles of chemoselectivity, site-selectivity, site-specificity, site-modularity, residue-modularity, and protein-specificity. With the knowledge to systematically regulate these parameters, the field has access to technological platforms that can address multiple challenges at the interface of chemistry, biology, and medicine.
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Affiliation(s)
- Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Neelesh C Reddy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, MP 462 066, India.
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14
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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15
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Mino T, Sakamoto S, Hamachi I. Recent applications of N-acyl imidazole chemistry in chemical biology. Biosci Biotechnol Biochem 2021; 85:53-60. [PMID: 33577657 DOI: 10.1093/bbb/zbaa026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
Abstract
N-Acyl imidazoles are unique electrophiles that exhibit moderate reactivity, relatively long-half life, and high solubility in water. Thanks to their tunable reactivity and chemical selectivity, the application of N-acyl imidazole derivatives has launched to a number of chemical biology researches, which include chemical synthesis of peptide/protein, chemical labeling of native proteins of interest (POIs), and structural analysis and functional manipulation of RNAs. Since proteins and RNAs play pivotal roles in numerous biological events in all living organisms, the methods that enable the chemical modification of endogenously existing POIs and RNAs in live cells may offer a variety of opportunities not only for fundamental scientific study but also for biotechnology and drug development. In this review, we discuss the recent progress of N-acyl imidazole chemistry that contributes to the chemical labeling and functional control of endogenous proteins and RNAs under multimolecularly crowded biological conditions of live cells.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.,ERATO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
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16
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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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17
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Amaike K, Oshima T, Skoulding NS, Toyama Y, Hirota T, Itami K. Small Molecules Modulating Mammalian Biological Clocks: Exciting New Opportunities for Synthetic Chemistry. Chem 2020. [DOI: 10.1016/j.chempr.2020.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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18
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Shiraiwa K, Cheng R, Nonaka H, Tamura T, Hamachi I. Chemical Tools for Endogenous Protein Labeling and Profiling. Cell Chem Biol 2020; 27:970-985. [DOI: 10.1016/j.chembiol.2020.06.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/29/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
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19
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Mizumoto S, Xi S, Fujiwara Y, Kawashima SA, Yamatsugu K, Kanai M. Hydroxamic Acid‐Piperidine Conjugate is an Activated Catalyst for Lysine Acetylation under Physiological Conditions. Chem Asian J 2020; 15:833-839. [DOI: 10.1002/asia.201901737] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/21/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Shinsuke Mizumoto
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Siqi Xi
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Fujiwara
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Shigehiro A. Kawashima
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical SciencesThe University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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20
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Reddy NC, Kumar M, Molla R, Rai V. Chemical methods for modification of proteins. Org Biomol Chem 2020; 18:4669-4691. [DOI: 10.1039/d0ob00857e] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.
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Affiliation(s)
- Neelesh C. Reddy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Mohan Kumar
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Rajib Molla
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
| | - Vishal Rai
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India
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21
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Nielsen T, Märcher A, Drobňáková Z, Hučko M, Štengl M, Balšánek V, Wiberg C, Nielsen PF, Nielsen TE, Gothelf KV, Cló E. Disulphide-mediated site-directed modification of proteins. Org Biomol Chem 2020; 18:4717-4722. [DOI: 10.1039/d0ob00861c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Site-directed addition of a single thiols handle to proteins by means of temporary disulphide rebridging of solvent exposed disulphides is obtained with a new labelling reagent.
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Affiliation(s)
- Thorbjørn Nielsen
- Interdisciplinary Nanoscience Center
- and the Dept. of Chemistry
- Aarhus University
- 8000 Aarhus C
- Denmark
| | - Anders Märcher
- Interdisciplinary Nanoscience Center
- and the Dept. of Chemistry
- Aarhus University
- 8000 Aarhus C
- Denmark
| | | | | | | | | | | | | | | | - Kurt V. Gothelf
- Interdisciplinary Nanoscience Center
- and the Dept. of Chemistry
- Aarhus University
- 8000 Aarhus C
- Denmark
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22
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Li Y, Lian C, Hou Z, Wang D, Wang R, Wan C, Zhong W, Zhao R, Wang Y, Li S, Yin F, Li Z. Intramolecular methionine alkylation constructs sulfonium tethered peptides for protein conjugation. Chem Commun (Camb) 2020; 56:3741-3744. [DOI: 10.1039/d0cc00377h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Continuous efforts have been invested in the selective modification of proteins.
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23
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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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24
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Shigenaga A. Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction. Chem Pharm Bull (Tokyo) 2019; 67:1171-1178. [PMID: 31685746 DOI: 10.1248/cpb.c19-00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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25
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Abstract
Template assistance allows organic reactions to occur under highly dilute conditions-where intermolecular reactions often fail to proceed-by bringing reactants into close spatial proximity. This strategy has been elegantly applied to numerous systems, but always with the retention of at least one of the templating groups in the product. In this report, we describe a traceless, templated amide-forming ligation that proceeds at low micromolar concentration under aqueous conditions in the presence of biomolecules. We utilized the unique features of an acylboronate-hydroxylamine ligation, in which covalent bonds are broken in each of the reactants as the new amide bond is formed. By using streptavidin as a template and acylboronates and O-acylhydroxylamines bearing desthiobiotins that are cleaved upon amide formation, we demonstrate that traceless, templated ligation occurs rapidly even at submicromolar concentrations. The requirement for a close spatial orientation of the functional groups-achieved upon binding to streptavidin-is critical for the observed enhancement in the rate and quantity of product formed.
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Affiliation(s)
- Alberto Osuna Gálvez
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
| | - Jeffrey W Bode
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences , ETH Zürich , 8093 Zürich , Switzerland
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26
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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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27
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Sakamoto S, Kiyonaka S, Hamachi I. Construction of ligand assay systems by protein-based semisynthetic biosensors. Curr Opin Chem Biol 2019; 50:10-18. [PMID: 30875618 DOI: 10.1016/j.cbpa.2019.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Abstract
Proteins as causative agents of diseases such as cancers, diabetes and neurological disorders are attractive drug targets. For developing chemicals selectively acting on key disease-causing proteins, one useful concept is the direct conversion of such target proteins into biosensors. This approach provides ligand-binding assay systems based on protein-based biosensors, which can quantitatively evaluate interactions between the protein and a specific ligand in many environments. Site-specific chemical modifications are used widely for the creation of protein-based semisynthetic biosensors in vitro. Notably, a few bio-orthogonal approaches capable of selectively modifying drug-targets have been developed, allowing conversion of specific target proteins into semisynthetic biosensors in live cells. These biosensors can be used for quantitative drug binding analyses in native environments. In this review, we discuss recent efforts for the construction of ligand assay systems using semisynthetic protein-based biosensors and their application to quantitative analysis and high-throughput screening of small molecules for drug discovery.
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Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - 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.
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28
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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29
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van der Zouwen AJ, Lohse J, Wieske LHE, Hohmann KF, van der Vlag R, Witte MD. An in situ combinatorial methodology to synthesize and screen chemical probes. Chem Commun (Camb) 2019; 55:2050-2053. [DOI: 10.1039/c8cc06991c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Linking of reactive groups and ligands by imine chemistry provides chemical probes that label proteins of interest.
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Affiliation(s)
- Antonie J. van der Zouwen
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Jonas Lohse
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Lianne H. E. Wieske
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Katharina F. Hohmann
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Ramon van der Vlag
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
| | - Martin D. Witte
- Chemical Biology II, Stratingh Institute for Chemistry, University of Groningen
- 9747AG Groningen
- The Netherlands
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30
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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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31
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Yamatsugu K, Furuta M, Xi S, Amamoto Y, Liu J, Kawashima SA, Kanai M. Kinetic analyses and structure-activity relationship studies of synthetic lysine acetylation catalysts. Bioorg Med Chem 2018; 26:5359-5367. [PMID: 30006145 DOI: 10.1016/j.bmc.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/20/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022]
Abstract
Lysine acylation of proteins is a crucial chemical reaction, both as a post-translational modification and as a method for bioconjugation. We previously developed a chemical catalyst, DSH, which activates a chemically stable thioester including acyl-CoA, allowing the site-selective lysine acylation of histones under physiological conditions. However, a more active catalyst is required for efficient lysine acylation in more complex biological milieu, such as in living cells, but there are no rational guidelines for developing efficient lysine acylation catalysts for use under physiological conditions as opposed to in organic solvents. We, herein, conducted a kinetic analysis of the ability of DSH and several derivatives to mediate lysine acetylation to better understand the structural elements essential for high acetylation activity under physiological conditions. Interestingly, the obtained trend in reactivity was different from that observed in organic solvents, suggesting that a different principle is necessary for designing chemical catalysts specifically for use under physiological conditions compared to catalysts for use in organic solvents. Based on the obtained information, we identified a new catalyst scaffold with high activity and structural flexibility for further modification to improve this catalyst system.
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Affiliation(s)
- Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan.
| | - Masahiro Furuta
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Siqi Xi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshifumi Amamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan
| | - Jiaan Liu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigehiro A Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; JST-ERATO, Japan.
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32
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Abstract
Chemically constructed biosensors consisting of a protein scaffold and an artificial small molecule have recently been recognized as attractive analytical tools for the specific detection and real-time monitoring of various biological substances or events in cells. Conventionally, such semisynthetic biosensors have been prepared in test tubes and then introduced into cells using invasive methods. With the impressive advances seen in bioorthogonal protein conjugation methodologies, however, it is now becoming feasible to directly construct semisynthetic biosensors in living cells, providing unprecedented tools for life-science research. We discuss here recent efforts regarding the in situ construction of protein-based semisynthetic biosensors and highlight their uses in the visualization and quantification of biomolecules and events in multimolecular and crowded cellular systems.
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Affiliation(s)
- Tsuyoshi Ueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- 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
- CREST(Core Research for Evolutional Science and Technology, JST), Sanbancho, Chiyodaku, Tokyo, 102-0075, Japan
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33
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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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