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Mou L, Yang L, Hou S, Wang B, Wang X, Hu L, Deng J, Liu J, Chen X, Jiang Y, Zhang W, Lei P, Wang L, Li R, Fu P, Li GB, Ma L, Yang L. Structure-Activity Relationship Studies of 2,4,5-Trisubstituted Pyrimidine Derivatives Leading to the Identification of a Novel and Potent Sirtuin 5 Inhibitor against Sepsis-Associated Acute Kidney Injury. J Med Chem 2023; 66:11517-11535. [PMID: 37556731 DOI: 10.1021/acs.jmedchem.3c01031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Sepsis-associated acute kidney injury (AKI) is a serious clinical problem without effective drugs. Inhibition of sirtuin 5 (SIRT5) has been confirmed to protect against AKI, suggesting that SIRT5 inhibitors might be a promising therapeutic approach for AKI. Herein, structural optimization was performed on our previous compound 1 (IC50 = 3.0 μM), and a series of 2,4,5-trisubstituted pyrimidine derivatives have been synthesized. The structure-activity relationship (SAR) analysis led to the discovery of three nanomolar level SIRT5 inhibitors, of which the most potent compound 58 (IC50 = 310 nM) was demonstrated to be a substrate-competitive and selective inhibitor. Importantly, 58 significantly alleviated kidney dysfunction and pathological injury in both lipopolysaccharide (LPS)- and cecal ligation/perforation (CLP)-induced septic AKI mice. Further studies revealed that 58 regulated protein succinylation and the release of proinflammatory cytokines in the kidneys of septic AKI mice. Collectively, these results highlighted that targeting SIRT5 has a therapeutic potential against septic AKI.
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Affiliation(s)
- Luohe Mou
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Lina Yang
- Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Shuyan Hou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Bo Wang
- Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Xinyue Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Lei Hu
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jianlin Deng
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jiayu Liu
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Xi Chen
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Yingying Jiang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Weifeng Zhang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Pengcheng Lei
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Lijiao Wang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Rong Li
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Ping Fu
- Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Liang Ma
- Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University, Chengdu 610039, China
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2
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Liu Z, Wu Y, Mao X, Kwan KCJ, Cheng X, Li X, Jing Y, Li XD. Development of multifunctional synthetic nucleosomes to interrogate chromatin-mediated protein interactions. SCIENCE ADVANCES 2023; 9:eade5186. [PMID: 37134166 PMCID: PMC10156118 DOI: 10.1126/sciadv.ade5186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Various proteins bind to chromatin to regulate DNA and its associated processes such as replication, transcription, and damage repair. The identification and characterization of these chromatin-associating proteins remain a challenge, as their interactions with chromatin often occur within the context of the local nucleosome or chromatin structure, which makes conventional peptide-based strategies unsuitable. Here, we developed a simple and robust protein labeling chemistry to prepare synthetic multifunctional nucleosomes that carry a photoreactive group, a biorthogonal handle, and a disulfide moiety to examine chromatin-protein interactions in a nucleosomal context. Using the prepared protein- and nucleosome-based photoaffinity probes, we examined a number of protein-protein and protein-nucleosome interactions. In particular, we (i) mapped the binding sites for the HMGN2-nucleosome interaction, (ii) provided the evidence for transition between the active and poised states of DOT1L in recognizing H3K79 within the nucleosome, and (iii) identified OARD1 and LAP2α as nucleosome acidic patch-associating proteins. This study provides powerful and versatile chemical tools for interrogating chromatin-associating proteins.
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Affiliation(s)
- Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiping Wu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Mao
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Xinxin Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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3
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Zhang Z, Lin J, Liu Z, Tian G, Li XM, Jing Y, Li X, Li XD. Photo-Cross-Linking To Delineate Epigenetic Interactome. J Am Chem Soc 2022; 144:20979-20997. [DOI: 10.1021/jacs.2c06135] [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)
- Zhuoyuan Zhang
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiao-Meng Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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4
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Wang S, Osgood AO, Chatterjee A. Uncovering post-translational modification-associated protein-protein interactions. Curr Opin Struct Biol 2022; 74:102352. [PMID: 35334254 DOI: 10.1016/j.sbi.2022.102352] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 02/05/2023]
Abstract
In living systems, the chemical space and functional repertoire of proteins are dramatically expanded through the post-translational modification (PTM) of various amino acid residues. These modifications frequently trigger unique protein-protein interactions (PPIs) - for example with reader proteins that directly bind the modified amino acid residue - which leads to downstream functional outcomes. The modification of a protein can also perturb its PPI network indirectly, for example, through altering its conformation or subcellular localization. Uncovering the network of unique PTM-triggered PPIs is essential to fully understand the roles of an ever-expanding list of PTMs in our biology. In this review, we discuss established strategies and current challenges associated with this endeavor.
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Affiliation(s)
- Shu Wang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Arianna O Osgood
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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5
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Ai H, Peng S, Li JB. Chemical methods for studying the crosstalk between histone H2B ubiquitylation and H3 methylation. J Pept Sci 2021; 28:e3381. [PMID: 34811838 DOI: 10.1002/psc.3381] [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: 07/17/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 11/06/2022]
Abstract
The reversible and dynamic post-translational modifications (PTMs) of histones in eukaryotic chromatin are intimately connected to cell development and gene function, and abnormal regulation of PTMs can result in cancer and neurodegenerative diseases. Specific combinations of these modifications are mediated by a series of chromatin proteins that write, erase, and read the "histone codes," but mechanistic studies of the precise biochemical and structural relationships between different sets of modifications and their effects on chromatin function constitute a unique challenge to canonical biochemical approaches. In the past decade, the development and application of chemical methods for investigating histone PTM crosstalks has received considerable attention in the field of chemical biology. In this review, taking the functional crosstalk between H2B ubiquitylation at Lys120 (H2BK120ub) and H3 methylation at Lys79 (H3K79me) as a typical example, we survey recent developments of different chemical methods, in particular, protein synthetic chemistry and protein-based chemical probes, for studying the mechanism of the functional crosstalks of histone PTMs.
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Affiliation(s)
- Huasong Ai
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Shuai Peng
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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6
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Ma H, Wu Y, Zhang W, Zhang H, Miao Z, Zhuang C. Radiosensitization of human pancreatic cancer by piperlongumine analogues. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.08.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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7
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Cipriano A, Sbardella G, Ciulli A. Targeting epigenetic reader domains by chemical biology. Curr Opin Chem Biol 2020; 57:82-94. [DOI: 10.1016/j.cbpa.2020.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 12/17/2022]
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9
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Air-tolerant direct reductive N-methylation of amines using formic acid via simple inorganic base catalysis. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.04.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Ren Y, Sun Q, Yuan Z, Jiang Y. Combined inhibition of HDAC and DNMT1 induces p85α/MEK-mediated cell cycle arrest by dual target inhibitor 208 in U937 cells. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.03.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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11
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Li X, Liu L, Li Y. 15th Chinese International Peptide Symposium. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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