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Eom T, Khan A. Hypersensitive azobenzenes: facile synthesis of clickable and cleavable azo linkers with tunable and high reducibility. Org Biomol Chem 2020; 18:420-424. [PMID: 31904038 DOI: 10.1039/c9ob02515d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The aim of this work is to show that by increasing the number of donor substituents in a donor/acceptor system, the sensitivity of the azobenzene linkage towards a reductive cleavage reaction can be enhanced to unprecedented high levels. For instance, in a triple-donor system, less than a second constitutes the half-life of the azo (N[double bond, length as m-dash]N) bond. Synthetic access to such redox active scaffolds is highly practical and requires only 1-2 synthetic steps. The fundamental molecular design is also adaptable. This is demonstrated through scaffold functionalization by azide, tetraethylene glycol, and biotin groups. The availability of the azide group is shown in a copper-free 'click' reaction suitable in context with protein conjugation and proteomics application. Finally, the clean nature of the scission process is demonstrated with the help of liquid chromatography coupled with mass analysis. This work, therefore, describes development of cleavable azobenzene linkers that can be accessed with synthetic ease, can be multiply functionalized, and show a clean and rapid response to mild reducing conditions.
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Affiliation(s)
- Taejun Eom
- Department of Chemical and Biological Engineering, Korea University, 145 Anam-Ro, Seongbuk-Gu, Seoul 02841, Korea.
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Eom T, Yoo W, Kim S, Khan A. Biologically activatable azobenzene polymers targeted at drug delivery and imaging applications. Biomaterials 2018; 185:333-347. [DOI: 10.1016/j.biomaterials.2018.09.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/30/2022]
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Yip AMH, Lo KKW. Luminescent rhenium(I), ruthenium(II), and iridium(III) polypyridine complexes containing a poly(ethylene glycol) pendant or bioorthogonal reaction group as biological probes and photocytotoxic agents. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.01.021] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Liew SS, Du S, Ge J, Pan S, Jang SY, Lee JS, Yao SQ. A chemoselective cleavable fluorescence turn-ON linker for proteomic studies. Chem Commun (Camb) 2017; 53:13332-13335. [DOI: 10.1039/c7cc08235e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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
We have developed a trifunctional cleavable fluorescence turn-ON linker for chemoproteomic applications.
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Affiliation(s)
- Si Si Liew
- Department of Chemistry
- National University of Singapore
- Singapore
| | - Shubo Du
- Department of Chemistry
- National University of Singapore
- Singapore
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- China
| | - Sijun Pan
- Department of Chemistry
- National University of Singapore
- Singapore
| | - Se-Young Jang
- Molecular Recognition Research Center & Department of Biological Chemistry
- KIST-School UST
- Korea Institute of Science & Technology
- South Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center & Department of Biological Chemistry
- KIST-School UST
- Korea Institute of Science & Technology
- South Korea
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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Choo JAL, Thong SY, Yap J, van Esch WJE, Raida M, Meijers R, Lescar J, Verhelst SHL, Grotenbreg GM. Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Choo JAL, Thong SY, Yap J, van Esch WJE, Raida M, Meijers R, Lescar J, Verhelst SHL, Grotenbreg GM. Bioorthogonal Cleavage and Exchange of Major Histocompatibility Complex Ligands by Employing Azobenzene-Containing Peptides. Angew Chem Int Ed Engl 2014; 53:13390-4. [DOI: 10.1002/anie.201406295] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/20/2014] [Indexed: 12/19/2022]
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Yang KS, Budin G, Tassa C, Kister O, Weissleder R. Bioorthogonal Approach to Identify Unsuspected Drug Targets in Live Cells. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Yang KS, Budin G, Tassa C, Kister O, Weissleder R. Bioorthogonal approach to identify unsuspected drug targets in live cells. Angew Chem Int Ed Engl 2013; 52:10593-7. [PMID: 23960025 DOI: 10.1002/anie.201304096] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/24/2013] [Indexed: 11/12/2022]
Abstract
A proteomics method to pull down secondary drug targets from live cells is described. The drug of interest is modified with trans-cyclooctene (TCO) and incubated with live cells. Upon cell lysis, the modified drug bound to the protein is pulled down using magnetic beads decorated with a cleavable tetrazine-modified linker. Samples are then run on an SDS-PAGE gel and isolated bands are submitted for mass spectrometry analysis to identify drug targets.
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Affiliation(s)
- Katherine S Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114 (USA)
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Rudolf GC, Heydenreuter W, Sieber SA. Chemical proteomics: ligation and cleavage of protein modifications. Curr Opin Chem Biol 2013; 17:110-7. [DOI: 10.1016/j.cbpa.2012.11.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 11/02/2012] [Indexed: 11/15/2022]
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Claessen JHL, Witte MD, Yoder NC, Zhu AY, Spooner E, Ploegh HL. Catch-and-release probes applied to semi-intact cells reveal ubiquitin-specific protease expression in Chlamydia trachomatis infection. Chembiochem 2013; 14:343-52. [PMID: 23335262 DOI: 10.1002/cbic.201200701] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 12/26/2022]
Abstract
Protein ubiquitylation controls many cellular pathways, and timely removal of ubiquitin by deubiquitylating enzymes (DUBs) is essential to govern these different functions. To map endogenous expression of individual DUBs as well as that of any interacting proteins, we developed a catch-and-release ubiquitin probe. Ubiquitin was equipped with an activity-based warhead and a cleavable linker attached to a biotin affinity-handle through tandem site-specific modification, in which we combined intein chemistry with sortase-mediated ligation. The resulting probe is cell-impermeable and was therefore delivered to the cytosol of perfringolysin O (PFO)-permeabilized cells. This allowed us to retrieve and identify 34 DUBs and their interacting partners. We also noted the expression, in host cells infected with Chlamydia trachomatis, of two additional DUBs. Furthermore, we retrieved and identified chlamydial DUB1 (ChlaDUB1) and DUB2 (ChlaDUB2), demonstrating by experiment that ChlaDUB2, the presence and activity of which had not been detected in infected cells, is in fact expressed during the course of infection.
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Affiliation(s)
- Jasper H L Claessen
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Martin D Witte
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Nicholas C Yoder
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Angela Y Zhu
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Eric Spooner
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142, Cambridge, MA, USA
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Leriche G, Chisholm L, Wagner A. Cleavable linkers in chemical biology. Bioorg Med Chem 2012; 20:571-82. [DOI: 10.1016/j.bmc.2011.07.048] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/08/2011] [Accepted: 07/23/2011] [Indexed: 01/11/2023]
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13
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Leriche G, Budin G, Darwich Z, Weltin D, Mély Y, Klymchenko AS, Wagner A. A FRET-based probe with a chemically deactivatable quencher. Chem Commun (Camb) 2012; 48:3224-6. [DOI: 10.1039/c2cc17542h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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