1
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Singh VP, Hirose S, Takemoto M, Farrag AMAS, Sato SI, Honjo T, Chamoto K, Uesugi M. Chemoproteomic Identification of Spermidine-Binding Proteins and Antitumor-Immunity Activators. J Am Chem Soc 2024. [PMID: 38848460 DOI: 10.1021/jacs.3c14615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Cancer immune therapies, particularly programmed cell death protein 1 (PD-1) blockade immunotherapy, falter in aged individuals due to compromised T-cell immunity. Spermidine, a biogenic polyamine that declines along with aging, shows promise in restoring antitumor immunity by enhancing mitochondrial fatty acid oxidation (FAO). Herein, we report a spermidine-based chemoproteomic probe (probe 2) that enables profiling of spermidine-binding proteins and screening for small-molecule enhancers of mitochondrial FAO. Chemoproteomic profiling by the probe revealed 140 proteins engaged in cellular interaction with spermidine, with a significant majority being mitochondrial proteins. Hydroxyl coenzyme A (CoA) dehydrogenase subunits α (HADHA) and other lipid metabolism-linked proteins are among the mitochondrial proteins that have attracted considerable interest. Screening spermidine analogs with the probe led to the discovery of compound 13, which interacts with these lipid metabolism-linked proteins and activates HADHA. This simple and biostable synthetic compound we named "spermimic" mirrors spermidine's ability to enhance mitochondrial bioenergetics and displays similar effectiveness in augmenting PD-1 blockade therapy in mice. This study lays the foundation for developing small-molecule activators of antitumor immunity, offering potential in combination cancer immunotherapy.
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Affiliation(s)
- Vaibhav Pal Singh
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Shuhei Hirose
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Misao Takemoto
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Asmaa M A S Farrag
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Shin-Ichi Sato
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tasuku Honjo
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Kenji Chamoto
- Division of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
- Department of Immuno-Oncology PDT, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Motonari Uesugi
- Division of Biochemistry, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Kyoto 606-8372, Japan
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2
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To HM, Ollevier T. Cyclopropanation of Alkenes with Halodiazirines as Halocarbene Precursors in Continuous Flow. Chemistry 2024; 30:e202303969. [PMID: 38490952 DOI: 10.1002/chem.202303969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
The cyclopropanation reaction of alkenes with photolytically-generated chlorocarbenes from chlorodiazirines is reported as an effective way to prepare substituted 3-chloro-3-aryl-cyclopropanes. This practical and efficient approach allows the synthesis of various 3-chloro-3-aryl-cyclopropanes (32 examples) in continuous flow in 5-minute residence time under light-emitting diode (LED) irradiation. The conditions using 380 nm LED irradiation were successfully extended to the synthesis of substituted 3-bromo-3-aryl-cyclopropanes (3 examples).
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Affiliation(s)
- Hoang-Minh To
- Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Thierry Ollevier
- Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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3
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Zhang C, Wan JP. Synthesis of Hypervalent Iodine Diazo Compounds and Their Application in Organic Synthesis. Chemistry 2024; 30:e202302718. [PMID: 37846841 DOI: 10.1002/chem.202302718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/18/2023]
Abstract
Diazomethyl-substituted iodine(III) compounds with electron-withdrawing groups (EWG) connected to diazo methyl center were a type of donor-acceptor diazo compounds with potential reaction abilities similar to ordinary diazo compounds. Although several diazomethyl-substituted iodine(III) compounds were synthesized and used in the nucleophilic substitution reactions as early as 1994, the synthesis and application of new iodine(III) diazo compounds have only been reported to a certain extent in recent years. In the presence of rhodium catalyst, photocatalyst, or nucleophiles, diazomethyl-substituted iodine(III) compounds can be converted into rhodium-carbenes, diazomethyl radicals, ester radicals or nucleophilic intermediates, which can be used as key intermediates for the formation of chemical bonds. The aim of this review is to give an overview of diazomethyl-substituted iodine(III) compounds in organic synthesis.
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Affiliation(s)
- Cai Zhang
- Department of Safety Supervision and Management, Chongqing Vocational Institute of Safety Technology, 583 Anqing road, Wanzhou district, 404020, Chongqing, China
| | - Jie-Ping Wan
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, 99 Ziyang Avenue, 330022, Nanchang, China
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4
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Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc 2024; 146:1337-1345. [PMID: 38165744 DOI: 10.1021/jacs.3c09545] [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: 01/04/2024]
Abstract
State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.
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Affiliation(s)
- David C Cabanero
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Stavros K Kariofillis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Andrew C Johns
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jinwoo Kim
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jizhi Ni
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sangho Park
- Discovery Biology, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Dann L Parker
- Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Carlo P Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Xavier Roy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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5
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Tureček F. Covalent crosslinking in gas-phase biomolecular ions. An account and perspective. Phys Chem Chem Phys 2023; 25:32292-32304. [PMID: 37990588 DOI: 10.1039/d3cp04879a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Photochemical crosslinking in gas-phase ion complexes has been introduced as a method to study biomolecular structures and dynamics. Emphasis has been on carbene-based crosslinking induced by photodissociation of diazirine-tagged ions. The features that characterize gas-phase crosslinking include (1) complex formation in electrospray droplets that allows for library-type screening; (2) well defined stoichiometry of the complexes due to mass-selective isolation; (3) facile reaction monitoring and yield determination, and (4) post-crosslinking structure analysis by tandem mass spectrometry that has been combined with hydrogen-deuterium exchange, UV-vis action spectroscopy, and ion mobility measurements. In this account, examples are given of peptide-peptide, peptide-nucleotide, and peptide-ligand crosslinking that chiefly used carbene-based reactions. The pros and cons of gas-phase crosslinking are discussed. Nitrile-imine based crosslinking in gas-phase ions is introduced as a promising new approach to ion structure analysis that offers high efficiency and has the potential for wide ranging applications.
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Affiliation(s)
- František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, WA 98195-1700, USA.
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6
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Maus H, Gellert A, Englert OR, Chen JX, Schirmeister T, Barthels F. Designing photoaffinity tool compounds for the investigation of the DENV NS2B-NS3 protease allosteric binding pocket. RSC Med Chem 2023; 14:2365-2379. [PMID: 37974966 PMCID: PMC10650954 DOI: 10.1039/d3md00331k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
Dengue virus (DENV) infection still lacks specific antiviral therapy, making the NS2B-NS3 protease an attractive target for drug development. However, allosteric inhibitors that bind to a site other than the active site still need to be better understood. In this study, we designed and synthesised tool compounds for photoaffinity labelling (PAL) to investigate the binding site of allosteric inhibitors on the DENV protease. These tool compounds contained an affinity moiety, a photoreactive group, and a reporter tag for detection. Upon irradiation, the photoreactive group formed a covalent bond with the protease, allowing for binding site identification. SDS-PAGE-based assays confirmed the qualitative binding of the designed inhibitors to the allosteric pocket, and pull-down experiments validated the interaction. Tryptic protein digestion following liquid chromatography/mass spectrometry analysis further supported the binding of the inhibitor to the proposed pocket revealing photo-attachment to an NS3 loop close to the C-terminus. These results enhance our understanding of allosteric inhibitors and their mechanism of action against the DENV protease. The developed tool compounds and PAL are potent tools for future drug discovery efforts and investigations targeting the DENV protease.
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Affiliation(s)
- Hannah Maus
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Andrea Gellert
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Olivia R Englert
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Jia-Xuan Chen
- IMB, Johannes Gutenberg-University Mainz Ackermannweg 4 55128 Mainz Germany
| | - Tanja Schirmeister
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- IPBS, Johannes Gutenberg-University Mainz Staudingerweg 5 55128 Mainz Germany
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7
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Zhang S, Liu P, Li L, Liu Z, Qian X, Jiang X, Sun W, Wang L, Akkaya EU. Upconverting Nanoparticle-Based Photoactive Probes for Highly Efficient Labeling and Isolation of Target Proteins. ACS APPLIED MATERIALS & INTERFACES 2023; 15:40280-40291. [PMID: 37585283 DOI: 10.1021/acsami.3c08397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Photoaffinity labeling (PAL) has blossomed into a powerful and versatile tool for capture and identification of biomolecular targets. However, low labeling efficiency for specific targets such as lectins, the tedious process for protein purification, inevitable cellular photodamage, and less tissue penetration of UV light are significant challenges. Herein, we reported a near-infrared (NIR) light-driven photoaffinity labeling approach using upconverting nanoparticle (UCNP)-based photoactive probes, which were constructed by assembling photoactive groups and ligands onto NaYF4:Yb,Tm nanoparticles. The novel probes were easily prepared and functionalized, and the labeled proteins can be isolated and purified through simple centrifugation and washing. The advantages of this approach were demonstrated by labeling and isolation of peanut agglutinin (PNA), asialoglycoprotein receptor (ASGPR), and human carbonic anhydrase II (hCAII) from mixed proteins or cell lysates with good selectivity and efficiency, especially for PNA and ASGPR, two lectins that showed low binding affinity to their ligands. More importantly, successful labeling of PNA through pork tissues and ASGPR in mice strongly proved the good tissue penetrating capacity of NIR light and the application potential of UCNP-based photoactive probes for protein labeling in vivo. Biosafety of this approach was experimentally validated by enzyme, cell, and animal work, and we demonstrated that NIR light caused minimal photodamage to enzyme activity compared to UV light, and the UCNP-based photoactive probe presents good biosafety both in vitro and in vivo. We believe that this novel PAL approach will provide a promising tool for study of ligand-protein interactions and identification of biomolecular targets.
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Affiliation(s)
- Shengli Zhang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Peng Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Li Li
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Ziang Liu
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xiao Qian
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xueying Jiang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Engin U Akkaya
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
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8
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Gibaut QR, Bush JA, Tong Y, Baisden JT, Taghavi A, Olafson H, Yao X, Childs-Disney JL, Wang ET, Disney MD. Transcriptome-Wide Studies of RNA-Targeted Small Molecules Provide a Simple and Selective r(CUG) exp Degrader in Myotonic Dystrophy. ACS CENTRAL SCIENCE 2023; 9:1342-1353. [PMID: 37521782 PMCID: PMC10375898 DOI: 10.1021/acscentsci.2c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 08/01/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is caused by a highly structured RNA repeat expansion, r(CUG)exp, harbored in the 3' untranslated region (3' UTR) of dystrophia myotonica protein kinase (DMPK) mRNA and drives disease through a gain-of-function mechanism. A panel of low-molecular-weight fragments capable of reacting with RNA upon UV irradiation was studied for cross-linking to r(CUG)expin vitro, affording perimidin-2-amine diazirine (1) that bound to r(CUG)exp. The interactions between the small molecule and RNA were further studied by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. Binding of 1 in DM1 myotubes was profiled transcriptome-wide, identifying 12 transcripts including DMPK that were bound by 1. Augmenting the functionality of 1 with cleaving capability created a chimeric degrader that specifically targets r(CUG)exp for elimination. The degrader broadly improved DM1-associated defects as assessed by RNA-seq, while having limited effects on healthy myotubes. This study (i) provides a platform to investigate molecular recognition of ligands directly in disease-affected cells; (ii) illustrates that RNA degraders can be more specific than the binders from which they are derived; and (iii) suggests that repeating transcripts can be selectively degraded due to the presence of multiple ligand binding sites.
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Affiliation(s)
- Quentin
M. R. Gibaut
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica A. Bush
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jared T. Baisden
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Amirhossein Taghavi
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hailey Olafson
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Xiyuan Yao
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jessica L. Childs-Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Eric T. Wang
- Center
for NeuroGenetics, University of Florida, Gainesville, Florida 32610, United States
- Department
of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Matthew D. Disney
- The
Department of Chemistry, UF Scripps Biomedical
Research and The Scripps Research Institute, Jupiter, Florida 33458, United States
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9
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Zhu H, Zima V, Ding ER, Tureček F. Carbene Cross-Linking in Gas-Phase Peptide Ion Scaffolds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:763-774. [PMID: 36881876 DOI: 10.1021/jasms.3c00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Scaffolds consisting of a peptide, a phthalate linker, and a 4,4-azipentyl group were synthesized and used to study intramolecular peptide-carbene cross-linking in gas-phase cations. Carbene intermediates were generated by UV-laser photodissociation at 355 nm of the diazirine ring in mass-selected ions, and the cross-linked products were detected and quantified by collision-induced dissociation tandem mass spectrometry (CID-MSn, n = 3-5). Peptide scaffolds containing Ala and Leu residues with a C-terminal Gly gave 21-26% yields of cross-linked products, while the presence of the Pro and His residues decreased the yields. Experiments using hydrogen-deuterium-hydrogen exchange, carboxyl group blocking, and analysis of CID-MSn spectra of reference synthetic products revealed that a significant fraction of cross-links involved the Gly amide and carboxyl groups. Interpretation of the cross-linking results was aided by Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations that allowed us to establish the protonation sites and conformations of the precursor ions. Analysis of long (100 ps) BOMD trajectories was used to count close contacts between the incipient carbene and peptide atoms, and the counting statistics was correlated with the results of gas-phase cross-linking.
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Affiliation(s)
- Hongyi Zhu
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Václav Zima
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - Emily R Ding
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, Washington 98195-1700, United States
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10
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Murai Y, Hashimoto M. Heteroaromatic Diazirines Are Essential Building Blocks for Material and Medicinal Chemistry. Molecules 2023; 28:molecules28031408. [PMID: 36771073 PMCID: PMC9921084 DOI: 10.3390/molecules28031408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In materials (polymer) science and medicinal chemistry, heteroaromatic derivatives play the role of the central skeleton in development of novel devices and discovery of new drugs. On the other hand, (3-trifluoromethyl)phenyldiazirine (TPD) is a crucial chemical method for understanding biological processes such as ligand-receptor, nucleic acid-protein, lipid-protein, and protein-protein interactions. In particular, use of TPD has increased in recent materials science to create novel electric and polymer devices with comparative ease and reduced costs. Therefore, a combination of heteroaromatics and (3-trifluoromethyl)diazirine is a promising option for creating better materials and elucidating the unknown mechanisms of action of bioactive heteroaromatic compounds. In this review, a comprehensive synthesis of (3-trifluoromethyl)diazirine-substituted heteroaromatics is described.
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Affiliation(s)
- Yuta Murai
- Graduate School of Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Correspondence: (Y.M.); (M.H.); Tel.: +81-11-706-9030 (Y.M.); +81-11-706-3849 (M.H.)
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11
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Wu X, Chen Y, Lu W, Jin R, Lu X. Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries. Bioconjug Chem 2022; 33:1818-1824. [PMID: 36197318 DOI: 10.1021/acs.bioconjchem.2c00421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries.
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Affiliation(s)
- Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yujie Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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12
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Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins. Bioorg Med Chem 2022; 62:116721. [PMID: 35358862 DOI: 10.1016/j.bmc.2022.116721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.
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13
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Abstract
Herein, we described an efficient method for the construction of highly functionalized diazirines from the carbohydrazide and diazo-substituted hypervalent iodine reagents. Unambiguous transformation has been designed with user applicable and easy practicable conditions. Remarkably, d-glucose, menthol, aspirin, proline, and lithocholic acid were efficiently diazirinated. Furthermore, the method is mild, robust, and highly selective, which successfully converted a variety of aryl, alkyl, benzyl, and heterocyclic hydrazides into the corresponding diazirine derivatives.
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Affiliation(s)
- Monish Arbaz Ansari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Ganesh Kumar
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Maya Shankar Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
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14
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Earley D, Guillou A, Klingler S, Fay R, Gut M, d’Orchymont F, Behmaneshfar S, Reichert L, Holland JP. Charting the Chemical and Mechanistic Scope of Light-Triggered Protein Ligation. JACS AU 2022; 2:646-664. [PMID: 35373206 PMCID: PMC8970001 DOI: 10.1021/jacsau.1c00530] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Indexed: 05/04/2023]
Abstract
The creation of discrete, covalent bonds between a protein and a functional molecule like a drug, fluorophore, or radiolabeled complex is essential for making state-of-the-art tools that find applications in basic science and clinical medicine. Photochemistry offers a unique set of reactive groups that hold potential for the synthesis of protein conjugates. Previous studies have demonstrated that photoactivatable desferrioxamine B (DFO) derivatives featuring a para-substituted aryl azide (ArN3) can be used to produce viable zirconium-89-radiolabeled monoclonal antibodies (89Zr-mAbs) for applications in noninvasive diagnostic positron emission tomography (PET) imaging of cancers. Here, we report on the synthesis, 89Zr-radiochemistry, and light-triggered photoradiosynthesis of 89Zr-labeled human serum albumin (HSA) using a series of 14 different photoactivatable DFO derivatives. The photoactive groups explore a range of substituted, and isomeric ArN3 reagents, as well as derivatives of benzophenone, a para-substituted trifluoromethyl phenyl diazirine, and a tetrazole species. For the compounds studied, efficient photochemical activation occurs inside the UVA-to-visible region of the electromagnetic spectrum (∼365-450 nm) and the photochemical reactions with HSA in water were complete within 15 min under ambient conditions. Under standardized experimental conditions, photoradiosynthesis with compounds 1-14 produced the corresponding 89ZrDFO-PEG3-HSA conjugates with decay-corrected isolated radiochemical yields between 18.1 ± 1.8% and 62.3 ± 3.6%. Extensive density functional theory (DFT) calculations were used to explore the reaction mechanisms and chemoselectivity of the light-induced bimolecular conjugation of compounds 1-14 to protein. The photoactivatable DFO-derivatives operate by at least five distinct mechanisms, each producing a different type of bioconjugate bond. Overall, the experimental and computational work presented here confirms that photochemistry is a viable option for making diverse, functionalized protein conjugates.
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15
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Bhatt M, Shende P. Surface patterning techniques for proteins on nano- and micro-systems: a modulated aspect in hierarchical structures. J Mater Chem B 2022; 10:1176-1195. [PMID: 35119060 DOI: 10.1039/d1tb02455h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The surface patterning of protein using fabrication or the external functionalization of structures demonstrates various applications in the biomedical field for bioengineering, biosensing and antifouling. This review article offers an outline of the existing advances in protein patterning technology with a special emphasis on the current physical and physicochemical methods, including stencil patterning, trap- and droplet-based microfluidics, and chemical modification of surfaces via photolithography, microcontact printing and scanning probe nanolithography. Different approaches are applied for the biological studies of recent trends for single-protein patterning technology, such as robotic printing, stencil printing and colloidal lithography, wherein the concepts of physical confinement, electrostatic and capillary forces, as well as dielectrophoretics, are summarised to understand the design approaches. Photochemical alterations with diazirine, nitrobenzyl and aryl azide functional groups for the implication of modified substrates, such as self-assembled monolayers functionalized with amino silanes, organosilanes and alkanethiols on gold surfaces, as well as topographical effects of patterning techniques for protein functionalization and orientation, are discussed. Analytical methods for the evaluation of protein functionality are also mentioned. Regarding their selectivity, protein pattering methods will be readily used to fabricate modified surfaces and target-specific delivery systems for the transportation of macromolecules such as streptavidin, and albumin. Future applications of patterning techniques include high-throughput screening, the evaluation of intracellular interactions, accurate screening and personalized treatments.
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Affiliation(s)
- Maitri Bhatt
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
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16
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Ollevier T, Carreras V. Emerging Applications of Aryl Trifluoromethyl Diazoalkanes and Diazirines in Synthetic Transformations. ACS ORGANIC & INORGANIC AU 2022; 2:83-98. [PMID: 36855460 PMCID: PMC9954246 DOI: 10.1021/acsorginorgau.1c00027] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aryl trifluoromethyl diazoalkanes and diazirines have become unique as reactants in synthetic methodology. As privileged compounds containing CF3 groups and ease of synthetic access, aryl trifluoromethyl diazoalkanes and diazirines have been highlighted for their versatility in applications toward a wide range of synthetic transformations. This Perspective highlights the synthetic applications of these reactants as precursors of stabilized metal carbenes, i.e., donor-acceptor-substituted ones.
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17
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Murai Y, Hashimoto M, Yoshida T, Puteri Tachrim Z. Design and Synthesis of 1,3-Bis(3-(trifluoromethyl)diazirin-3-yl)phenylalanine for Efficient Photo Cross-Linking. HETEROCYCLES 2022. [DOI: 10.3987/com-21-14563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Musolino SF, Mahbod M, Nazir R, Bi L, Graham HA, Milani AS, Wulff JE. Electronically optimized diazirine-based polymer crosslinkers. Polym Chem 2022. [DOI: 10.1039/d2py00687a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronically optimized bis-diazirine crosslinkers allow aliphatic polymers to be crosslinked with up to 10-fold improved efficacy, relative to earlier designs. Activation is achieved using modest temperatures or through UV or visible light.
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Affiliation(s)
- Stefania F. Musolino
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Mahshid Mahbod
- Materials and Manufacturing Research Institute (MMRI), University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Rashid Nazir
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Liting Bi
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Hamish A. Graham
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Abbas S. Milani
- Materials and Manufacturing Research Institute (MMRI), University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Jeremy E. Wulff
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
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19
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Kamoshita S, Matsui S, Suto N, Sakurai K. Reactivity Analysis of New Multivalent Electrophilic Probes for Affinity Labeling of Carbohydrate Binding Proteins. Chembiochem 2021; 23:e202100388. [PMID: 34490706 DOI: 10.1002/cbic.202100388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/05/2021] [Indexed: 11/07/2022]
Abstract
We have designed and synthesized six different multivalent electrophiles as carbohydrate affinity labeling probes. Evaluation of the reactivity of the electrophiles against peanut agglutinin (PNA) and Ricinus communis agglutinin (RCA) showed that p- and m-aryl sulfonyl fluoride are effective protein reactive groups that label carbohydrate binding lectins in a ligand-dependent fashion at a nanomolar probe concentration. Analysis of the selectivity of affinity labeling in the presence of excess BSA as a nonspecific protein indicated that m-arylsulfonyl fluoride is a more selective protein-reactive group, albeit with attenuated reactivity. Further analysis showed that the labeling efficiency of the multivalent electrophilic probes can be improved by employing reaction conditions involving 25 °C instead of typically employed 4 °C. Both isomers of arylsulfonyl fluoride groups together represent promising affinity labels for target identification studies that could serve as more efficient alternatives to photoreactive groups.
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Affiliation(s)
- Shione Kamoshita
- Department of Bioengineering and Life Science, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Saho Matsui
- Department of Bioengineering and Life Science, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Nanako Suto
- Department of Bioengineering and Life Science, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Kaori Sakurai
- Department of Bioengineering and Life Science, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
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20
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Tachrim ZP, Wang L, Murai Y, Hashimoto M. New Trends in Diaziridine Formation and Transformation (a Review). Molecules 2021; 26:4496. [PMID: 34361648 PMCID: PMC8348119 DOI: 10.3390/molecules26154496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 01/18/2023] Open
Abstract
This review focuses on diaziridine, a high strained three-membered heterocycle with two nitrogen atoms that plays an important role as one of the most important precursors of diazirine photoaffinity probes, as well as their formation and transformation. Recent research trends can be grouped into three categories, based on whether they have examined non-substituted, N-monosubstituted, or N,N-disubstituted diaziridines. The discussion expands on the conventional methods for recent applications, the current spread of studies, and the unconventional synthesis approaches arising over the last decade of publications.
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Affiliation(s)
- Zetryana Puteri Tachrim
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- Research Center for Chemistry, Indonesian Institute of Sciences, Kawasan Puspiptek, Serpong, South Tangerang 15314, Banten, Indonesia
| | - Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- State Key Laboratory of Fine Chemicals, Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Yuta Murai
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
- Frontier Research Center for Post-Genome Science and Technology, Faculty of Advanced Life Science, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo 001-0021, Japan
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (L.W.); (Y.M.)
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21
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Suto N, Kamoshita S, Hosoya S, Sakurai K. Exploration of the Reactivity of Multivalent Electrophiles for Affinity Labeling: Sulfonyl Fluoride as a Highly Efficient and Selective Label. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Nanako Suto
- Department of Bioengineering and Life Science Tokyo University of Agriculture and Technology 4-24-16, Naka-cho, Koganei-shi Tokyo 184-8588 Japan
| | - Shione Kamoshita
- Department of Bioengineering and Life Science Tokyo University of Agriculture and Technology 4-24-16, Naka-cho, Koganei-shi Tokyo 184-8588 Japan
| | - Shoichi Hosoya
- Institute of Research Tokyo Medical and Dental University 1-5-45, Yushima, Bunkyo-ku Tokyo 113-8510 Japan
| | - Kaori Sakurai
- Department of Bioengineering and Life Science Tokyo University of Agriculture and Technology 4-24-16, Naka-cho, Koganei-shi Tokyo 184-8588 Japan
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22
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Suto N, Kamoshita S, Hosoya S, Sakurai K. Exploration of the Reactivity of Multivalent Electrophiles for Affinity Labeling: Sulfonyl Fluoride as a Highly Efficient and Selective Label. Angew Chem Int Ed Engl 2021; 60:17080-17087. [PMID: 34060195 DOI: 10.1002/anie.202104347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Indexed: 12/23/2022]
Abstract
Here we explored the reactivity of a set of multivalent electrophiles cofunctionalized with a carbohydrate ligand on gold nanoparticles to achieve efficient affinity labeling for target protein analysis. Evaluation of the reactivity and selectivity of the electrophiles against three different cognate binding proteins identified arylsulfonyl fluoride as the most efficient protein-reactive group in this study. We demonstrated that multivalent arylsulfonyl fluoride probe 4 at 50 nm concentration achieved selective affinity labeling and enrichment of a model protein PNA in cell lysate, which was more effective than photoaffinity probe 1 with arylazide group. Labeling site analysis by LC-MS/MS revealed that the nanoparticle-immobilized arylsulfonyl fluoride group can target multiple amino acid residues around the ligand binding site of the target proteins. Our study highlights the utility of arylsulfonyl fluoride as a highly effective multivalent affinity label suitable for covalently capturing unknown target proteins.
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Affiliation(s)
- Nanako Suto
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Shione Kamoshita
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
| | - Shoichi Hosoya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kaori Sakurai
- Department of Bioengineering and Life Science, Tokyo University of Agriculture and Technology, 4-24-16, Naka-cho, Koganei-shi, Tokyo, 184-8588, Japan
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23
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Schwickert K, Andrzejewski M, Grabowsky S, Schirmeister T. Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands. J Org Chem 2021; 86:6169-6183. [PMID: 33835801 DOI: 10.1021/acs.joc.0c02993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via 19F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.
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Affiliation(s)
- Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Michał Andrzejewski
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Simon Grabowsky
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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24
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Hashimoto M, Nakagita T, Misaka T. Recent progress in the use of diaziridine-based sweetener derivatives to elucidate the chemoreception mechanism of the sweet taste receptor. RSC Adv 2021; 11:32236-32247. [PMID: 35495529 PMCID: PMC9041848 DOI: 10.1039/d1ra04831g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/21/2021] [Indexed: 11/21/2022] Open
Abstract
The review summarized recent progress for the elucidation of the chemoreception mechanism of sweet taste receptor–sweetener interactions with photoaffinity labeling.
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Affiliation(s)
- Makoto Hashimoto
- Division of Applied Science, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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25
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Hashimoto M, Hashinoki M, Kurokawa N, Murai Y, Puteri Tachrim Z, Sakihama Y, Suzuki T. Synthesis of (Trifluoromethyldiazirinyl)phenylboronic Acid Derivatives for Photoaffinity Labeling. HETEROCYCLES 2021. [DOI: 10.3987/com-20-s(k)23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Chandrachud PP, Wojtas L, Lopchuk JM. Decarboxylative Amination: Diazirines as Single and Double Electrophilic Nitrogen Transfer Reagents. J Am Chem Soc 2020; 142:21743-21750. [PMID: 33332115 DOI: 10.1021/jacs.0c09403] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ubiquity of nitrogen-containing small molecules in medicine necessitates the continued search for improved methods for C-N bond formation. Electrophilic amination often requires a disparate toolkit of reagents whose selection depends on the specific structure and functionality of the substrate to be aminated. Further, many of these reagents are challenging to handle, engage in undesired side reactions, and function only within a narrow scope. Here we report the use of diazirines as practical reagents for the decarboxylative amination of simple and complex redox-active esters. The diaziridines thus produced are readily diversifiable to amines, hydrazines, and nitrogen-containing heterocycles in one step. The reaction has also been applied in fluorous phase synthesis with a perfluorinated diazirine.
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Affiliation(s)
- Preeti P Chandrachud
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Justin M Lopchuk
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States.,Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States.,Department of Oncologic Sciences, College of Medicine, University of South Florida, Tampa, Florida 33612, United States
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27
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Madasu J, Shinde S, Das R, Patel S, Shard A. Potassium tert-butoxide mediated C-C, C-N, C-O and C-S bond forming reactions. Org Biomol Chem 2020; 18:8346-8365. [PMID: 33020791 DOI: 10.1039/d0ob01382j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Potassium tertiary butoxide (KOtBu) mediated constructions of C-C, C-O, C-N, and C-S bonds are reviewed with special emphasis on their synthetic applications. KOtBu can be used to perform reactions already known to be carried out using transition metals, but it has advantages in terms of environmental congruence and economic cost. KOtBu is widely employed in organic synthesis to mediate the construction of C-C, C-O, C-N, C-S and miscellaneous bonds in good to excellent yields. Synthetic uses of KOtBu in coupling, alkylation, arylation, α-phenylation, cyclization, Heck-type, annulation, photo-arylation, aromatic-substitution, amidation, and silylation reactions are summarized and discussed. The mechanisms through which KOtBu carries out a specific reaction are also discussed. One of the goals of this review is to attract the attention of chemists as to the benefits of using KOtBu as an environmentally benign alternative to transition metals and its applications in the construction of chemical bonds with predominant importance in organic synthesis. This review completely covers the synthetic protocols that have been performed using KOtBu in the last two decades.
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Affiliation(s)
- Jayashree Madasu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India.
| | - Shital Shinde
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India.
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India.
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India.
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gujarat 380054, India.
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28
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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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29
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Nakagita T, Ishida A, Tachrim ZP, Wang L, Misaka T, Hashimoto M. Asymmetric Synthesis of Photophore-Containing Lactisole Derivatives to Elucidate Sweet Taste Receptors. Molecules 2020; 25:molecules25122790. [PMID: 32560345 PMCID: PMC7355818 DOI: 10.3390/molecules25122790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 11/23/2022] Open
Abstract
Lactisole, which has a 2-phenoxy propionic acid skeleton, is well-known as an inhibitor of sweet taste receptors. We recently revealed some of the structure–activity relationships of the aromatic ring and chiral center of lactisole. Photoaffinity labeling is one of the common chemical biology methods to elucidate the interaction between bioactive compounds and biomolecules. In this paper, the novel asymmetric synthesis of lactisole derivatives with common photophores (benzophenone, azide and trifluoromethyldiazirine) for photoaffinity labeling is described. The synthetic compounds are subjected to cell-based sweet taste receptors, and the substitution with trifluoromethyldiazirinyl photophore shows the highest affinity to the receptor of the synthesized compounds.
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Affiliation(s)
- Tomoya Nakagita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; (T.N.); (T.M.)
- Proteo-Science Center, Ehime University, Ehime 791-8577, Japan
| | - Akiko Ishida
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (A.I.); (Z.P.T.); (L.W.)
| | - Zetryana Puteri Tachrim
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (A.I.); (Z.P.T.); (L.W.)
- Program Study of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132, Indonesia
| | - Lei Wang
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (A.I.); (Z.P.T.); (L.W.)
- Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116023, China
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; (T.N.); (T.M.)
| | - Makoto Hashimoto
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan; (A.I.); (Z.P.T.); (L.W.)
- Correspondence: ; Tel.: +81-11-7063849
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30
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Wang C, Liu Y, Bao C, Xue Y, Zhou Y, Zhang D, Lin Q, Zhu L. Phototriggered labeling and crosslinking by 2-nitrobenzyl alcohol derivatives with amine selectivity. Chem Commun (Camb) 2020; 56:2264-2267. [PMID: 31984385 DOI: 10.1039/c9cc09449k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we report the use of 2-nitrobenzyl alcohol (NB) as a photoreactive group with amine selectivity and explore its applications for photoaffinity labeling and crosslinking of biomolecules. This work confirms that NB is an efficient photoreactive group and has great potential in drug discovery, chemical biology and protein engineering.
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Affiliation(s)
- Chenxi Wang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yuan Liu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Chunyan Bao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yuan Xue
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Yaowu Zhou
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Dasheng Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Qiuning Lin
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
| | - Linyong Zhu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry & Molecular Engineering, East China University of Science & Technology, Shanghai, 200237, P. R. China.
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31
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Park H, Zhang G, Bae J, Theis T, Warren WS, Wang Q. Application of 15N 2-Diazirines as a Versatile Platform for Hyperpolarization of Biological Molecules by d-DNP. Bioconjug Chem 2020; 31:537-541. [PMID: 32023034 DOI: 10.1021/acs.bioconjchem.0c00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
15N2-Diazirines represent an attractive class of imaging tags for hyperpolarized magnetic resonance imaging (HP-MRI), offering desirable biocompatibility, ease of incorporation into a variety of molecules, and ability to deliver long-lasting polarization. We have recently established hyperpolarization of 15N2-diazirines in organic solvents using SABRE-Shield Enables Alignment Transfer to Heteronuclei (SABRE-SHEATH). Yet, the current challenge of SABRE-SHEATH in water, specifically poor polarization efficiency, presents a barrier in examining the practical use of 15N2-diazirines for HP-MRI. Herein, we show that efficient polarization of diverse 15N2-diazirine-labeled molecules in water can be readily achieved by dissolution dynamic nuclear polarization (d-DNP), a hyperpolarization technique used in clinical practice. Hyperpolarization by d-DNP also demonstrates greater enhancement for long-lasting 15N signals, in comparison with SABRE-SHEATH. Various biologically important molecules are studied in this work, including amino acid, sugar, and drug compounds, demonstrating the great potential of 15N2-diazirines as molecular tags in broad biomedical and clinical applications.
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Affiliation(s)
- Hyejin Park
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Guannan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Junu Bae
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Thomas Theis
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Warren S Warren
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Radiology and Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Qiu Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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32
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Wang H, Xu R, Liang S, Ran F, Zhang L, Zhang Y, Zhou D, Xiao S. Selective and facile deacetylation of pentacyclic triterpenoid under methanolic ammonia condition and unambiguous NMR analysis. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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33
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Djordjevic I, Wicaksono G, Solic I, Steele TW. Diazoalkane decay kinetics from UVA-active protein labelling molecules: Trifluoromethyl phenyl diazirines. RESULTS IN CHEMISTRY 2020. [DOI: 10.1016/j.rechem.2020.100066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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34
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Saaidin AS, Murai Y, Ishikawa T, Monde K. Design and Synthesis of Ligand-Tag Exchangeable Photoaffinity Probe Utilizing Nosyl Chemistry. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Aimi Suhaily Saaidin
- Graduate School of Life Science; Hokkaido University; Kita 11 Nishi 21 001-0021 Sapporo Japan
| | - Yuta Murai
- Faculty of Advanced Life Science; Hokkaido University; Kita 21 Nishi 11 001-0021 Sapporo Japan
| | - Takuya Ishikawa
- Graduate School of Life Science; Hokkaido University; Kita 11 Nishi 21 001-0021 Sapporo Japan
| | - Kenji Monde
- Faculty of Advanced Life Science; Hokkaido University; Kita 21 Nishi 11 001-0021 Sapporo Japan
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35
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Xu J, Li X, Ding K, Li Z. Applications of Activity-Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery. Chem Asian J 2019; 15:34-41. [PMID: 31762171 DOI: 10.1002/asia.201901500] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 01/12/2023]
Abstract
Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.
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Affiliation(s)
- Jiaqian Xu
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR, 999077, China
| | - Xiaoqian Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
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36
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Holland JP, Gut M, Klingler S, Fay R, Guillou A. Photochemical Reactions in the Synthesis of Protein-Drug Conjugates. Chemistry 2019; 26:33-48. [PMID: 31599057 DOI: 10.1002/chem.201904059] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 12/15/2022]
Abstract
The ability to modify biologically active molecules such as antibodies with drug molecules, fluorophores or radionuclides is crucial in drug discovery and target identification. Classic chemistry used for protein functionalisation relies almost exclusively on thermochemically mediated reactions. Our recent experiments have begun to explore the use of photochemistry to effect rapid and efficient protein functionalisation. This article introduces some of the principles and objectives of using photochemically activated reagents for protein ligation. The concept of simultaneous photoradiosynthesis of radiolabelled antibodies for use in molecular imaging is introduced as a working example. Notably, the goal of producing functionalised proteins in the absence of pre-association (non-covalent ligand-protein binding) introduces requirements that are distinct from the more regular use of photoactive groups in photoaffinity labelling. With this in mind, the chemistry of thirteen different classes of photoactivatable reagents that react through the formation of intermediate carbenes, electrophiles, dienes, or radicals, is assessed.
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Affiliation(s)
- Jason P Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Melanie Gut
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Klingler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amaury Guillou
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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37
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Fan CY, Hou YR, Adak AK, Waniwan JT, Dela Rosa MAC, Low PY, Angata T, Hwang KC, Chen YJ, Lin CC. Boronate affinity-based photoactivatable magnetic nanoparticles for the oriented and irreversible conjugation of Fc-fused lectins and antibodies. Chem Sci 2019; 10:8600-8609. [PMID: 31803435 PMCID: PMC6844280 DOI: 10.1039/c9sc01613a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/31/2019] [Indexed: 12/29/2022] Open
Abstract
The utilization of immuno-magnetic nanoparticles (MNPs) for the selective capture, enrichment, and separation of specific glycoproteins from complicated biological samples is appealing for the discovery of disease biomarkers. Herein, MNPs were designed and anchored with abundant boronic acid (BA) and photoreactive alkyl diazirine (Diaz) functional groups to obtain permanently tethered Fc-fused Siglec-2 and antiserum amyloid A (SAA) mAb with the assistance of reversible boronate affinity and UV light activation in an orientation-controlled manner. The Siglec-2-Fc-functionalized MNPs showed excellent stability in fetal bovine serum (FBS) and excellent efficiency in the extraction of cell membrane glycoproteins. The anti-SAA mAb-functionalized MNPs maintained active Ab orientation and preserved antigen recognition capability in biological samples. Thus, the BA-Diaz-based strategy holds promise for the immobilization of glycoproteins, such as antibodies, with the original protein binding activity maintained, which can provide better enrichment for the sensitive detection of target proteins.
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Affiliation(s)
- Chen-Yo Fan
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan .
| | - Yi-Ren Hou
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan .
| | - Avijit K Adak
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan .
| | | | | | - Penk Yeir Low
- Institute of Biological Chemistry , Academia Sinica , Taipei , Taiwan
| | - Takashi Angata
- Institute of Biological Chemistry , Academia Sinica , Taipei , Taiwan
| | - Kuo-Chu Hwang
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan .
| | - Yu-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei , Taiwan .
| | - Chun-Cheng Lin
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan .
- Frontier Research Center on Fundamental and Applied Sciences of Matters , Hsinchu , Taiwan
- Department of Medicinal and Applied Chemistry , Kaohsiung Medical University , Kaohsiung , Taiwan
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38
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Komatsu R, Sakurai K. Development of Chemical Probes for Functional Analysis of Anticancer Saponin OSW‐1. CHEM REC 2019; 19:2362-2369. [DOI: 10.1002/tcr.201900042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/17/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Rina Komatsu
- Department of Biotechnology and Life Science Faculty of EngineeringTokyo University of Agriculture and Technology 2-28-16, Nakacho, Koganei-shi Tokyo 184-8588 Japan
| | - Kaori Sakurai
- Department of Biotechnology and Life Science Faculty of EngineeringTokyo University of Agriculture and Technology 2-28-16, Nakacho, Koganei-shi Tokyo 184-8588 Japan
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39
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Glachet T, Marzag H, Saraiva Rosa N, Colell JFP, Zhang G, Warren WS, Franck X, Theis T, Reboul V. Iodonitrene in Action: Direct Transformation of Amino Acids into Terminal Diazirines and 15N 2-Diazirines and Their Application as Hyperpolarized Markers. J Am Chem Soc 2019; 141:13689-13696. [PMID: 31373802 DOI: 10.1021/jacs.9b07035] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A one-pot metal-free conversion of unprotected amino acids to terminal diazirines has been developed using phenyliodonium diacetate (PIDA) and ammonia. This PIDA-mediated transformation occurs via three consecutive reactions and involves an iodonitrene intermediate. This method is tolerant to most functional groups found on the lateral chain of amino acids, it is operationally simple, and it can be scaled up to provide multigram quantities of diazirine. Interestingly, we also demonstrated that this transformation could be applied to dipeptides without racemization. Furthermore, 14N2 and 15N2 isotopomers can be obtained, emphasizing a key trans-imination step when using 15NH3. In addition, we report the first experimental observation of 14N/15N isotopomers directly creating an asymmetric carbon. Finally, the 15N2-diazirine from l-tyrosine was hyperpolarized by a parahydrogen-based method (SABRE-SHEATH), demonstrating the products' utility as hyperpolarized molecular tag.
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Affiliation(s)
- Thomas Glachet
- Normandie Univ , ENSICAEN, UNICAEN, CNRS, LCMT , 14000 Caen , France
| | - Hamid Marzag
- Normandie Univ , ENSICAEN, UNICAEN, CNRS, LCMT , 14000 Caen , France
| | | | - Johannes F P Colell
- Department of Chemistry , Duke University , 124 Science Drive , Durham , North Carolina 27708 , United States
| | - Guannan Zhang
- Department of Chemistry , Duke University , 124 Science Drive , Durham , North Carolina 27708 , United States
| | - Warren S Warren
- Department of Chemistry , Duke University , 124 Science Drive , Durham , North Carolina 27708 , United States
| | - Xavier Franck
- Normandie Univ , CNRS, UNIROUEN, INSA Rouen, COBRA , 76000 Rouen , France
| | - Thomas Theis
- Department of Chemistry , Duke University , 124 Science Drive , Durham , North Carolina 27708 , United States.,Department of Chemistry , North Carolina State University , 2620 Yarbrough Drive , Raleigh , North Carolina 27695 , United States
| | - Vincent Reboul
- Normandie Univ , ENSICAEN, UNICAEN, CNRS, LCMT , 14000 Caen , France
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40
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Lim B, Lee J, Kim B, Lee R, Park J, Oh D, Gam J, Lee J. Target Identification of a 1,3,4‐Oxadiazin‐5(6
H
)‐One Anticancer Agent via Photoaffinity Labelling. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Bumhee Lim
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jinah Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Byungjin Kim
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Rang Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jaehyun Park
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Dong‐Chan Oh
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
| | - Jongsik Gam
- Department of Medicinal BioscienceCollege of Interdisciplinary & Creative StudiesKonyang University 2121 Daehak-ro Nonsan, Chungnam 32992 Korea
| | - Jeeyeon Lee
- College of PharmacyResearch Institute of Pharmaceutical sciencesSeoul National University 1 Gwanak-ro, Gwanak-gu Seoul 08826 Korea
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41
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Stoytcheva M, Zlatev R, Velkova Z, Gochev V, Ayala A, Montero G, Valdez B. Diazirine‐functionalized Nanostructured Platform for Enzymes Photografting and Electrochemical Biosensing. ELECTROANAL 2019. [DOI: 10.1002/elan.201900086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
| | - Roumen Zlatev
- Universidad Autónoma de Baja CaliforniaInstituto de Ingeniería Mexicali México
| | - Zdravka Velkova
- Medical University of PlovdivFaculty of Pharmacy, Dep. Chemical Sciences Plovdiv Bulgaria
| | - Velizar Gochev
- Plovdiv University “P. Hilendarski”Faculty of Biology, Dep. Biochemistry and Microbiology Plovdiv Bulgaria
| | - Alan Ayala
- Universidad Autónoma de Baja CaliforniaInstituto de Ingeniería Mexicali México
| | - Gisela Montero
- Universidad Autónoma de Baja CaliforniaInstituto de Ingeniería Mexicali México
| | - Benjamín Valdez
- Universidad Autónoma de Baja CaliforniaInstituto de Ingeniería Mexicali México
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42
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Hellerstedt J, Cahlík A, Stetsovych O, Švec M, Shimizu TK, Mutombo P, Klívar J, Stará IG, Jelínek P, Starý I. Aromatic Azide Transformation on the Ag(111) Surface Studied by Scanning Probe Microscopy. Angew Chem Int Ed Engl 2019; 58:2266-2271. [DOI: 10.1002/anie.201812334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Jack Hellerstedt
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
| | - Aleš Cahlík
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Oleksander Stetsovych
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
- National Institute for Materials Science (NIMS) 1-2-1 Sengen Tsukuba 305-0047 Japan
| | - Martin Švec
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Tomoko K. Shimizu
- National Institute for Materials Science (NIMS) 1-2-1 Sengen Tsukuba 305-0047 Japan
| | - Pingo Mutombo
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
| | - Jiří Klívar
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences of the Czech Republic Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences of the Czech Republic Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Pavel Jelínek
- Institute of PhysicsAcademy of Sciences of the Czech Republic Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and MaterialsFaculty of SciencePalacký University Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and BiochemistryAcademy of Sciences of the Czech Republic Flemingovo nám. 2 16610 Prague 6 Czech Republic
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43
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Hellerstedt J, Cahlík A, Stetsovych O, Švec M, Shimizu TK, Mutombo P, Klívar J, Stará IG, Jelínek P, Starý I. Aromatic Azide Transformation on the Ag(111) Surface Studied by Scanning Probe Microscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jack Hellerstedt
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
| | - Aleš Cahlík
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Faculty of Science; Palacký University; Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Oleksander Stetsovych
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
- National Institute for Materials Science (NIMS); 1-2-1 Sengen Tsukuba 305-0047 Japan
| | - Martin Švec
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Faculty of Science; Palacký University; Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Tomoko K. Shimizu
- National Institute for Materials Science (NIMS); 1-2-1 Sengen Tsukuba 305-0047 Japan
| | - Pingo Mutombo
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
| | - Jiří Klívar
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Pavel Jelínek
- Institute of Physics; Academy of Sciences of the Czech Republic; Cukrovarnická 10 16200 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Faculty of Science; Palacký University; Šlechtitelû 27 78371 Olomouc Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo nám. 2 16610 Prague 6 Czech Republic
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44
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Masuda M, Matsuo K, Hamachi I. Ligand-Directed N-Sulfonyl Pyridone Chemistry for Selective Native Protein Labeling and Imaging in Live Cell. Methods Mol Biol 2019; 2008:203-224. [PMID: 31124099 DOI: 10.1007/978-1-4939-9537-0_16] [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: 12/31/2022]
Abstract
Advances in biocompatible organic chemistry applicable for endogenous protein modification under live-cell conditions have been longed as these can produce an important tool for the elucidation of a variety of biological phenomena. However, there are still various obstacles to be overcome, such as the limited repertories of the reaction modes, the slow reaction kinetics, and the insufficient specificity for endogenous protein modification. We have recently reported a new type of affinity-based labeling technique termed ligand-directed (LD) chemistry that does not need any genetic manipulation, which shows a sharp contrast with other strategies including peptide/enzyme-tag methods or bioorthogonal chemistry-based methods. Here we describe the general principles of LD chemistry using N-sulfonyl pyridone (SP) as a new reactive group (LDSP chemistry) that allows for endogenous protein sulfonylation with the higher labeling rate and specificity, relative to our previously reported LD chemistry on the surface of and the inside of live cells. The detailed protocols of LDSP chemistry for carbonic anhydrase labeling and imaging in vitro and in living cells are explained.
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Affiliation(s)
- Marie Masuda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kazuya Matsuo
- Research Institute for Electronic Science, Hokkaido University, Hokkaido, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan. .,Japan Science and Technology Agency (JST), ERATO, Tokyo, Japan.
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45
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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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46
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Hamilton CM, Hung M, Chen G, Qureshi Z, Thompson JR, Sun B, Bear CE, Young RN. Synthesis and characterization of a photoaffinity labelling probe based on the structure of the cystic fibrosis drug ivacaftor. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Beiroth F, Koudelka T, Overath T, Knight SD, Tholey A, Lindhorst TK. Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH. Beilstein J Org Chem 2018; 14:1890-1900. [PMID: 30112094 PMCID: PMC6071696 DOI: 10.3762/bjoc.14.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/27/2018] [Indexed: 12/27/2022] Open
Abstract
Photoaffinity labeling is frequently employed for the investigation of ligand–receptor interactions in solution. We have employed an interdisciplinary methodology to achieve facile photolabeling of the lectin FimH, which is a bacterial protein, crucial for adhesion, colonization and infection. Following our earlier work, we have here designed and synthesized diazirine-functionalized mannosides as high-affinity FimH ligands and performed an extensive study on photo-crosslinking of the best ligand (mannoside 3) with a series of model peptides and FimH. Notably, we have employed high-performance mass spectrometry to be able to detect radiation results with the highest possible accuracy. We are concluding from this study that photolabeling of FimH with sugar diazirines has only very limited success and cannot be regarded a facile approach for covalent modification of FimH.
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Affiliation(s)
- Femke Beiroth
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24118 Kiel, Germany
| | - Tomas Koudelka
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Thorsten Overath
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Stefan D Knight
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala, Sweden
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany
| | - Thisbe K Lindhorst
- Otto Diels Institute of Organic Chemistry, Christiana Albertina University of Kiel, Otto-Hahn-Platz 3/4, 24118 Kiel, Germany
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Hill JR, Robertson AAB. Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis. J Med Chem 2018; 61:6945-6963. [PMID: 29683660 DOI: 10.1021/acs.jmedchem.7b01561] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.
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Affiliation(s)
- James R Hill
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia
| | - Avril A B Robertson
- Institute for Molecular Bioscience , The University of Queensland , St. Lucia , Queensland 4072 , Australia.,School of Chemistry and Molecular Biosciences , The University of Queensland , St. Lucia QLD4072 , Australia
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Affiliation(s)
- Arun Babu Kumar
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
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Novel biotin linker with alkyne and amino groups for chemical labelling of a target protein of a bioactive small molecule. Bioorg Med Chem Lett 2018; 28:783-786. [PMID: 29306572 DOI: 10.1016/j.bmcl.2017.12.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 11/24/2022]
Abstract
We synthesized a novel linker (1) with biotin, alkyne and amino groups for the identification of target proteins using a small molecule that contains an azide group (azide probe). The alkyne in the linker bound the azide probe via an azide-alkyne Huisgen cycloaddition. A protein cross-linker effectively bound the conjugate of the linker and an azide probe with a target protein. The covalently bound complex was detected by western blotting. Linker 1 was applied to a model system using an abscisic acid receptor, RCAR/PYR/PYL (PYL). Cross-linked complexes of linker 1, the azide probes and the target proteins were successfully visualized by western blotting. This method of target protein identification was more effective than a previously developed method that uses a second linker with biotin, alkyne, and benzophenone (linker 2) that acts to photo-crosslink target proteins. The system developed in this study is a method for identifying the target proteins of small bioactive molecules and is different from photo-affinity labelling.
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