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Otaka A. Development of Naturally Inspired Peptide and Protein Chemistry. Chem Pharm Bull (Tokyo) 2022; 70:748-764. [DOI: 10.1248/cpb.c22-00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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Shigenaga A. Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction. Chem Pharm Bull (Tokyo) 2019; 67:1171-1178. [PMID: 31685746 DOI: 10.1248/cpb.c19-00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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3
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Shigenaga A. [Looking Back on Study Abroad at The Scripps Research Institute]. YAKUGAKU ZASSHI 2019; 139:221-228. [PMID: 30713231 DOI: 10.1248/yakushi.18-00169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Just after receiving my Ph.D. degree in 2004 from Tokushima University, under the supervision of Professor Masayuki Shibuya, I had the opportunity to work as a Research Associate in the laboratory of Professor Kim D. Janda at The Scripps Research Institute in the U.S., for about a year. Since it has already been more than 10 years since my time at Scripps, the specific research performed at that time may no longer be of interest to readers, but the benefit of working in a different research environment is timeless. Therefore, this paper describes not only details of the research conducted, but also the significance of working in a foreign country as a postdoc, and the subsequent influence those experiences at The Scripps Research Institute have had on my career.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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Mahesh S, Tang KC, Raj M. Amide Bond Activation of Biological Molecules. Molecules 2018; 23:E2615. [PMID: 30322008 PMCID: PMC6222841 DOI: 10.3390/molecules23102615] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 12/02/2022] Open
Abstract
Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.
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Affiliation(s)
- Sriram Mahesh
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
| | - Kuei-Chien Tang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
| | - Monika Raj
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA.
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Okoh OA, Klahn P. Trimethyl Lock: A Multifunctional Molecular Tool for Drug Delivery, Cellular Imaging, and Stimuli-Responsive Materials. Chembiochem 2018; 19:1668-1694. [PMID: 29888433 DOI: 10.1002/cbic.201800269] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 12/13/2022]
Abstract
Trimethyl lock (TML) systems are based on ortho-hydroxydihydrocinnamic acid derivatives displaying increased lactonization reactivity owing to unfavorable steric interactions of three pendant methyl groups, and this leads to the formation of hydrocoumarins. Protection of the phenolic hydroxy function or masking of the reactivity as benzoquinone derivatives prevents lactonization and provides a trigger for controlled release of molecules attached to the carboxylic acid function through amides, esters, or thioesters. Their easy synthesis and possible chemical adaption to several different triggers make TML a highly versatile module for the development of drug-delivery systems, prodrug approaches, cell-imaging tools, molecular tools for supramolecular chemistry, as well as smart stimuliresponsive materials.
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Affiliation(s)
- Okoh Adeyi Okoh
- Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Philipp Klahn
- Institute for Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
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Affiliation(s)
- Masato Ikeda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193
| | - Marina Kabumoto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193
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Shigenaga A, Yamamoto J, Kohiki T, Inokuma T, Otaka A. Invention of stimulus-responsive peptide-bond-cleaving residue (Spr) and its application to chemical biology tools. J Pept Sci 2017; 23:505-513. [PMID: 28105728 DOI: 10.1002/psc.2961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 01/04/2023]
Abstract
Elucidation of biological functions of peptides and proteins is essential for understanding peptide/protein-related biological events and developing drugs. Caged peptides and proteins that release a parent active peptide/protein by photo-irradiation have successfully been employed to elucidate the functions. Whereas the usual caged peptide/protein enables conversion of an inactive form to an active form (OFF-to-ON conversion) by photo-induced deprotection, photo-triggered main chain cleavage is reported to be applicable to ON-to-OFF conversion. These peptides and proteins are photo-responsive; however, if peptides and proteins could respond to other stimuli such as disease-related environment or enzymes, their range of application should be widened. To convert the photo-responsive peptide/protein into other stimulus-responsive peptide/protein, quite laborious de novo design and synthesis of the stimulus-responsive unit are required. In this context, we designed a stimulus-responsive peptide-bond-cleaving residue (Spr) in which the stimuli available for the main chain cleavage vary according to the choice of protecting groups on the residue. In this review, design and synthesis of Spr are introduced, and challenges to apply Spr to other fields to enable, for example, functional control, localization control, delivery of cargos, labeling of a protein of interest in living cells, and identification of target proteins of bioactive ligands are discussed. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Jun Yamamoto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Taiki Kohiki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Tsubasa Inokuma
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
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Kita M, Yamamoto J, Morisaki T, Komiya C, Inokuma T, Miyamoto L, Tsuchiya K, Shigenaga A, Otaka A. Design and synthesis of a hydrogen peroxide-responsive amino acid that induces peptide bond cleavage after exposure to hydrogen peroxide. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yamamoto J, Denda M, Maeda N, Kita M, Komiya C, Tanaka T, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a traceable linker containing a thiol-responsive amino acid for the enrichment and selective labelling of target proteins. Org Biomol Chem 2015; 12:3821-6. [PMID: 24806338 DOI: 10.1039/c4ob00622d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A traceable linker that is potentially applicable to identification of a target protein of bioactive compounds was developed. It enabled not only thiol-induced cleavage of the linker for enrichment of the target protein but also selective labelling to pick out the target from contaminated non-target proteins for facile identification.
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Affiliation(s)
- Jun Yamamoto
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan.
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Yamamoto J, Maeda N, Komiya C, Tanaka T, Denda M, Ebisuno K, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a fluoride-responsive amide bond cleavage device that is potentially applicable to a traceable linker. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Shigenaga A. [Development of stimulus-responsive amino acids and their application to chemical biology use]. YAKUGAKU ZASSHI 2012; 132:1075-82. [PMID: 23023427 DOI: 10.1248/yakushi.132.1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An understanding of the physiological significance of peptides and proteins is indispensable in the fields of life sciences and drug development. Recently, methods for controlling peptide and protein activities using stimuli such as UV irradiation have been attracting much attention because of their potential for clarifying the physiological roles of the peptides/proteins. In this context, we have developed a stimulus-responsive amino acid that induces peptide-bond cleavage after exposure to a stimulus. Although it has previously been reported that stimulus-responsive units can respond to a specific stimulus, our stimulus-responsive amino acid is potentially applicable to any stimulus simply by changing the protective group. In this review, the design and synthesis of stimulus-responsive amino acids are described. Their applications in chemical biology, including their use for spatiotemporal control of the activity of peptides in living cells, are also reported.
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Affiliation(s)
- Akira Shigenaga
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Tokushima, Japan.
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Shigenaga A, Ogura K, Hirakawa H, Yamamoto J, Ebisuno K, Miyamoto L, Ishizawa K, Tsuchiya K, Otaka A. Development of a Reduction-Responsive Amino Acid that Induces Peptide Bond Cleavage in Hypoxic Cells. Chembiochem 2012; 13:968-71. [DOI: 10.1002/cbic.201200141] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Indexed: 02/04/2023]
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Levine MN, Raines RT. Trimethyl lock: A trigger for molecular release in chemistry, biology, and pharmacology. Chem Sci 2012; 3:2412-2420. [PMID: 23181187 PMCID: PMC3501758 DOI: 10.1039/c2sc20536j] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The trimethyl lock is an o-hydroxydihydrocinnamic acid derivative in which unfavorable steric interactions between three pendant methyl groups encourage lactonization to form a hydrocoumarin. This reaction is extremely rapid, even when the electrophile is an amide and the leaving group is an amino group of a small-molecule drug, fluorophore, peptide, or nucleic acid. O-Acylation of the phenolic hydroxyl group prevents reaction, providing a trigger for the reaction. Thus, the release of an amino group from an amide can be coupled to the hydrolysis of a designated ester (or to another chemical reaction that regenerates the hydroxyl group). Trimethyl lock conjugates are easy to synthesize, making the trimethyl lock a highly versatile module for chemical biology and related fields.
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Affiliation(s)
- Michael N. Levine
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706, USA
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Design and synthesis of caged ceramide: UV-responsive ceramide releasing system based on UV-induced amide bond cleavage followed by O–N acyl transfer. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.04.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shigenaga A, Yamamoto J, Nishioka N, Otaka A. Enantioselective synthesis of stimulus-responsive amino acid via asymmetric α-amination of aldehyde. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.07.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Shigenaga A, Yamamoto J, Sumikawa Y, Furuta T, Otaka A. Development and photo-responsive peptide bond cleavage reaction of two-photon near-infrared excitation-responsive peptide. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.03.079] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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