1
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Chen J, Wang Y, Wang R, Yuan R, Chu GC, Li YM. Chemical synthesis of on demand-activated SUMO-based probe by a photocaged glycine-assisted strategy. Bioorg Med Chem Lett 2023; 94:129460. [PMID: 37640164 DOI: 10.1016/j.bmcl.2023.129460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/05/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
The transiently-activated SUMO probes are conducive to understand the dynamic control of SENPs activity. Here, we developed a photocaged glycine-assisted strategy for the construction of on demand-activated SUMO-ABPs. The light-sensitive groups installed at G92 and G64 backbone of SUMO-2 can temporarily block probes activity and hamper aspartimide formation, respectively, which enabled the efficient synthesis of inert SUMO-2 propargylamide (PA). The probe could be activated to capture SENPs upon photo-irradiation not only in vitro but also in intact cells, providing opportunities to further perform intracellular time-resolved proteome-wide profiling of SUMO-related enzymes.
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Affiliation(s)
- Jingnan Chen
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Yu Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
| | - Rongtian Wang
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Rujing Yuan
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China
| | - Guo-Chao Chu
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
| | - Yi-Ming Li
- School of Food and Biological Engineering, Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, China.
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2
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Hua X, Guo Y, Wang Y, Chu GC, Li P, Shi J. Acyl azide modification of the ubiquitin C-terminus enables DUB capture. Chem Commun (Camb) 2023; 59:1333-1336. [PMID: 36645155 DOI: 10.1039/d2cc06496k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Deubiquitinating enzyme (DUB) abnormalities are associated with many diseases. Previous attempts have been made to introduce various chemical groups such as alkynes, unsaturated olefins and alkyl halides to the C-terminus of ubiquitin (Ub) to capture the active-site cysteine residue in DUBs for structural and biochemical studies. Here, we find that a Ub C-terminal acyl azide can capture DUBs, thereby forming thioester bonds in buffers and cell lysates. This finding not only makes ubiquitin acyl azide a chemical probe for capturing DUBs, but also extends the utility of azide groups in biological applications.
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Affiliation(s)
- Xiao Hua
- Department of Chemistry, Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China.
| | - Yanyan Guo
- Department of Chemistry, Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China.
| | - Yu Wang
- Department of Chemistry, Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China.
| | - Guo-Chao Chu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Pincheng Li
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, 230009, China
| | - Jing Shi
- Department of Chemistry, Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China.
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3
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Wang Y, Xia Q, Hua X, Guo Y, Shi J, Li YM. Semi-synthesis of biotin-bearing activity-based Ubiquitin probes through sequential enzymatic ligation, N-S acyl transfer and aminolysis reaction. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Wang L, Zhang J, Shen W, Zeng X, Lee HK, Tang S. Can Direct-Immersion Aqueous–Aqueous Microextraction Be Achieved When Using a Single-Drop System? Anal Chem 2022; 94:12538-12545. [DOI: 10.1021/acs.analchem.2c03017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lina Wang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
| | - Xuemin Zeng
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
| | - Hian Kee Lee
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, PR China
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5
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022; 61:e202203792. [DOI: 10.1002/anie.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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Wang Y, Chen J, Hua X, Meng X, Cai H, Wang R, Shi J, Deng H, Liu L, Li Y. Photocaging of Activity‐Based Ubiquitin Probes via a C‐Terminal Backbone Modification Strategy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yu Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Jingnan Chen
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Xiao Hua
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Xianbin Meng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Hongyi Cai
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Rongtian Wang
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
| | - Jing Shi
- Department of Chemistry University of Science and Technology of China Hefei 230026 China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Department of Chemistry Tsinghua University Beijing 100084 China
| | - Yi‐Ming Li
- School of Food and Biological Engineering Engineering Research Center of Bio-process Ministry of Education Hefei University of Technology Hefei 230009 China
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Lu Y, Ji R, Ye Y, Hua X, Fan J, Xu Y, Shi J, Li YM. Efficient semi-synthesis of ubiquitin-fold modifier 1 (UFM1) derivatives. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Abstract
CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL)1015LausanneSwitzerland
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9
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Xu L, Zhang Y, Li YM, Lu XF. Total chemical synthesis of the phosphorylated p62 UBA domain reveals that Ser 407Pi but not Ser 403Pi enhances ubiquitin binding. Org Biomol Chem 2020; 18:8709-8715. [PMID: 33084718 DOI: 10.1039/d0ob01906b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As an autophagic adaptor, p62 specifically targets ubiquitinated proteins to an autophagosome for lysosomal degradation through a critical ubiquitin-associated (UBA) domain. Recent research studies reported that the Ser403 and Ser407 sites on the UBA domain were modified by phosphorylation, increasing the binding affinity between p62 and ubiquitin (Ub). However, the exact role of each phosphorylation site in the regulation of the UBA domain and Ub binding remains unclear. In this text, we applied total chemical synthesis to prepare four types of phosphorylated UBAs, among which the bisphosphorylated UBA was successfully synthesized via the pseudo-dipeptide unit and auxiliary-mediated hydrazide-based native chemical ligation (NCL). Isothermal titration calorimetry (ITC) assays showed that the phosphorylation at S407 enhanced the binding affinity between UBA and Ub, while that at S403 did not. It was suggested that phosphorylation at S407 might be important for promoting the interplay between the UBA domain and Ub, whereas phosphorylation at S403 was not directly involved in this interaction.
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Affiliation(s)
- Ling Xu
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
| | - Yan Zhang
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xian-Fu Lu
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
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N-benzylpiperidinol derivatives as novel USP7 inhibitors: Structure-activity relationships and X-ray crystallographic studies. Eur J Med Chem 2020; 199:112279. [PMID: 32497973 DOI: 10.1016/j.ejmech.2020.112279] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
USP7 as a deubiquitinase plays important roles in regulating the stability of some oncoproteins including MDM2 and DNMT1, and thus represents a potential anticancer target. Through comparative analysis of USP7 co-crystal structures in complex with the reported piperidinol inhibitors, we noticed that the USP7 Phe409 sub-site might have good adaptability to the ligands. Based on this observation, 55 N-aromatic and N-benzyl piperidinol derivatives were designed, synthesized and biologically evaluated, among which compound L55 was identified as a highly selective and potent USP7 inhibitor (IC50 = 40.8 nM, KD = 78.3 nM). X-ray crystallographic studies revealed that L55 bound to USP7 with a new pose that was very different from the previously reported inhibitors. The results of cellular assays showed that L55 had strong antitumor activity against LNCaP (IC50 = 29.6 nM) and RS4; 11 (IC50 = 41.6 nM) cells, probably through inducing cell death and restricting G0/G1 and S phases. Moreover, L55 dose-dependently reduced the protein levels of MDM2 and DNMT1 and increased the protein levels of p53 and p21. These findings could have valuable implications for designing novel structural classes of USP7 inhibitors.
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11
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Hua X, Bai JS, Kong YF, Chu GC, Shi J, Li YM. Acid-sensitive auxiliary assisted atypical diubiquitin synthesis exploiting thiol-ene coupling. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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