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Son S, Song WJ. Programming interchangeable and reversible heterooligomeric protein self-assembly using a bifunctional ligand. Chem Sci 2024; 15:2975-2983. [PMID: 38404387 PMCID: PMC10882485 DOI: 10.1039/d3sc05448a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024] Open
Abstract
Protein design for self-assembly allows us to explore the emergence of protein-protein interfaces through various chemical interactions. Heterooligomers, unlike homooligomers, inherently offer a comprehensive range of structural and functional variations. Besides, the macromolecular repertoire and their applications would significantly expand if protein components could be easily interchangeable. This study demonstrates that a rationally designed bifunctional linker containing an enzyme inhibitor and maleimide can guide the formation of diverse protein heterooligomers in an easily applicable and exchangeable manner without extensive sequence optimizations. As proof of concept, we selected four structurally and functionally unrelated proteins, carbonic anhydrase, aldolase, acetyltransferase, and encapsulin, as building block proteins. The combinations of two proteins with the bifunctional linker yielded four two-component heterooligomers with discrete sizes, shapes, and enzyme activities. Besides, the overall size and formation kinetics of the heterooligomers alter upon adding metal chelators, acidic buffer components, and reducing agents, showing the reversibility and tunability in the protein self-assembly. Given that the functional groups of both the linker and protein components are readily interchangeable, our work broadens the scope of protein-assembled architectures and their potential applications as functional biomaterials.
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Affiliation(s)
- Soyeun Son
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
| | - Woon Ju Song
- Department of Chemistry, College of Natural Sciences, Seoul National University Seoul 08826 Republic of Korea
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2
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Huang C, Shu Y, Zhu Y, Liu H, Wang X, Wen H, Liu J, Li W. Discovery of non-substrate, environmentally sensitive turn-on fluorescent probes for imaging HDAC8 in tumor cells and tissue slices. Bioorg Med Chem 2022; 68:116821. [PMID: 35661851 DOI: 10.1016/j.bmc.2022.116821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022]
Abstract
Histone deacetylase 8 (HDAC8) is overexpressed in multiple cancers and lack of effective chemical probes which could detect and visualize HDAC8 in tumor cells and tissues remains unsolved. In this work, three novel turn-on HDAC8 fluorescent probes 17-19 derived from solvatochromic fluorophore 4-sulfamonyl-7-aminobenzoxadiazole (SBD) conjugating with a potent HDAC8 inhibitor PCI-34051 (IC50 = 10 nM) as the recognition group were fabricated. The probes exhibited much stronger fluorescence when they transfer from hydrophilic environment (Φ < 8%) to hydrophobic environment (Φ > 46%). Compared with PCI-34051 (KD = 9.16 × 10-6 M), probes 17 (KD = 5.37 × 10-6 M), 18 (KD = 3.57 × 10-6 M) and 19 (KD = 8.89 × 10-6 M) possessed slightly better affinity for HDAC8. Probe 19 was selected for cell imaging and it showed significantly enhanced fluorescence only after binding into the cavity of HDAC8 in SH-SY5Y and MDA-MB-231 tumor cells. Co-localization results demonstrated that HDAC8 is expressed in cytoplasm and nucleus. Furthermore, probe 19 was successfully utilized to distinguish the expression level of HDAC8 in SH-SY5Y tumor and normal tissue slices.
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Affiliation(s)
- Chaoqun Huang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi Shu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yueyue Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hongjing Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xinzhi Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hongmei Wen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wei Li
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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3
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Mehta R, Rivera DD, Reilley DJ, Tan D, Thomas PW, Hinojosa A, Stewart AC, Cheng Z, Thomas CA, Crowder MW, Alexandrova AN, Fast W, Que EL. Visualizing the Dynamic Metalation State of New Delhi Metallo-β-lactamase-1 in Bacteria Using a Reversible Fluorescent Probe. J Am Chem Soc 2021; 143:8314-8323. [PMID: 34038127 DOI: 10.1021/jacs.1c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) grants resistance to a broad spectrum of β-lactam antibiotics, including last-resort carbapenems, and is emerging as a global antibiotic resistance threat. Limited zinc availability adversely impacts the ability of NDM-1 to provide resistance, but a number of clinical variants have emerged that are more resistant to zinc scarcity (e.g., NDM-15). To provide a novel tool to better study metal ion sequestration in host-pathogen interactions, we describe the development of a fluorescent probe that reports on the dynamic metalation state of NDM within Escherichia coli. The thiol-containing probe selectively coordinates the dizinc metal cluster of NDM and results in a 17-fold increase in fluorescence intensity. Reversible binding enables competition and time-dependent studies that reveal fluorescence changes used to detect enzyme localization, substrate and inhibitor engagement, and changes to metalation state through the imaging of live E. coli using confocal microscopy. NDM-1 is shown to be susceptible to demetalation by intracellular and extracellular metal chelators in a live-cell model of zinc dyshomeostasis, whereas the NDM-15 metalation state is shown to be more resistant to zinc flux. The development of this reversible turn-on fluorescent probe for the metalation state of NDM provides a new tool for monitoring the impact of metal ion sequestration by host defense mechanisms and for detecting inhibitor-target engagement during the development of therapeutics to counter this resistance determinant.
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Affiliation(s)
- Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Dann D Rivera
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - David J Reilley
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Emily L Que
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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4
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Pratt EPS, Damon LJ, Anson KJ, Palmer AE. Tools and techniques for illuminating the cell biology of zinc. Biochim Biophys Acta Mol Cell Res 2020; 1868:118865. [PMID: 32980354 DOI: 10.1016/j.bbamcr.2020.118865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Zinc (Zn2+) is an essential micronutrient that is required for a wide variety of cellular processes. Tools and methods have been instrumental in revealing the myriad roles of Zn2+ in cells. This review highlights recent developments fluorescent sensors to measure the labile Zn2+ pool, chelators to manipulate Zn2+ availability, and fluorescent tools and proteomics approaches for monitoring Zn2+-binding proteins in cells. Finally, we close with some highlights on the role of Zn2+ in regulating cell function and in cell signaling.
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Affiliation(s)
- Evan P S Pratt
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Leah J Damon
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Kelsie J Anson
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America
| | - Amy E Palmer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States of America.
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Wei T, Lu S, Sun J, Xu Z, Yang X, Wang F, Ma Y, Shi YS, Chen X. Sanger's Reagent Sensitized Photocleavage of Amide Bond for Constructing Photocages and Regulation of Biological Functions. J Am Chem Soc 2020; 142:3806-3813. [PMID: 32023409 DOI: 10.1021/jacs.9b11357] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photolabile groups offer promising tools to study biological processes with high spatial and temporal control. In the investigation, we designed and prepared several new glycine amide derivatives of Sanger's reagent and demonstrated that they serve as a new class of photocages for Zn2+ and an acetylcholinesterase (AChE) inhibitor. We showed that the mechanism for photocleavage of these substances involves initial light-driven cyclization between the 2,4-dinitrophenyl and glycine methylene groups to form acyl benzimidazole N-oxides, which undergo secondary photoinduced decarboxylation in association with rupture of an amide bond. The cleavage reactions proceed with modest to high quantum yields. We demonstrated that these derivatives can be used in targeted intracellular delivery of Zn2+, fluorescent imaging by light-triggered Zn2+ release, and regulation of biological processes including the enzymatic activity of carbonic anhydrase (CA), negative regulation of N-methyl-d-aspartate receptors (NMDARs), and pulse rate of cardiomyocytes. The successful proof-of-concept examples described above open a new avenue for using Sanger's reagent-based glycine amides as photocages for the exploration of complex cellular functions and signaling pathways.
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Affiliation(s)
- Tingwen Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Sheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Jiahui Sun
- State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , Nanjing 210032 , China.,Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center , Nanjing University , Nanjing 210032 , China
| | - Zhijun Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Xiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Fang Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Yang Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , Nanjing 210032 , China.,Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center , Nanjing University , Nanjing 210032 , China.,Chemistry and Biomedicine Innovation Center , Nanjing University , Nanjing 210032 , China
| | - Xiaoqiang Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
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Ngo C, Mehta R, Aggarwal K, Fikes AG, Santos IC, Greer SM, Que EL. Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes. Chembiochem 2019; 20:1003-1007. [PMID: 30520207 PMCID: PMC6530555 DOI: 10.1002/cbic.201800613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 11/07/2022]
Abstract
One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn2+ -containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.
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Affiliation(s)
- Chinh Ngo
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Kanchan Aggarwal
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Audrey G. Fikes
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Ines C. Santos
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Emily L. Que
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
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7
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2018; 35:702-706. [PMID: 30058659 DOI: 10.1039/c8np90024h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as pepluanol C from Euphorbia peplus.
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Affiliation(s)
- Robert A Hill
- School of Chemistry, Glasgow University, Glasgow, UKG12 8QQ.
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8
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Yan R, Wang Z, Du Z, Wang H, Cheng X, Xiong J. A biomimetic fluorescent chemosensor for highly sensitive zinc(ii) detection and its application for cell imaging. RSC Adv 2018; 8:33361-33367. [PMID: 35548108 PMCID: PMC9086477 DOI: 10.1039/c8ra06501b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/18/2018] [Indexed: 02/05/2023] Open
Abstract
To fabricate a novel biomimetic fluorescent chemosensor, PSaAEMA-co-PMPC was synthesized via atom transfer radical polymerization, and this copolymer could be used for the detection of zinc(ii) and cell imaging. A series tests with various metal ions verified the specific fluorescence response behavior. This novel biomimetic fluorescent chemosensor exhibits excellent selectivity for Zn2+ ions over a wide range of tested metal ions in an aqueous solution. Moreover, cytotoxicity and bio-imaging tests were conducted to study the potential bio-application of the chemosensor. Owing to the biomimetic portion (phosphorylcholine), this copolymer possesses outstanding biocompatibility and could clearly image cells. The results indicated that PSaAEMA-co-PMPC has great potential for application in zinc(ii) detection and cell imaging. To fabricate a novel biomimetic fluorescent chemosensor, PSaAEMA-co-PMPC was synthesized via atom transfer radical polymerization, and this copolymer could be used for the detection of zinc(ii) and cell imaging.![]()
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Affiliation(s)
- Rui Yan
- Textile Institute
- College of Light Industry
- Textile and Food Engineering
- Sichuan University
- Chengdu
| | - Zhi Wang
- State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu 610041
- China
| | - Zongliang Du
- Textile Institute
- College of Light Industry
- Textile and Food Engineering
- Sichuan University
- Chengdu
| | - Haibo Wang
- Textile Institute
- College of Light Industry
- Textile and Food Engineering
- Sichuan University
- Chengdu
| | - Xu Cheng
- Textile Institute
- College of Light Industry
- Textile and Food Engineering
- Sichuan University
- Chengdu
| | - Junjie Xiong
- Department of Pancreatic Surgery
- West China Hospital
- Sichuan University
- Chengdu 610041
- China
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