1
|
Chen C, Chen C, Wang A, Jiang Z, Zhao F, Li Y, Han Y, Niu Z, Tian S, Bai X, Zhang K, Zhai G. ENL reads histone β-hydroxybutyrylation to modulate gene transcription. Nucleic Acids Res 2024:gkae504. [PMID: 38880495 DOI: 10.1093/nar/gkae504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/03/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Histone modifications are typically recognized by chromatin-binding protein modules (referred to as 'readers') to mediate fundamental processes such as transcription. Lysine β-hydroxybutyrylation (Kbhb) is a new type of histone mark that couples metabolism to gene expression. However, the readers that prefer histone Kbhb remain elusive. This knowledge gap should be filled in order to reveal the molecular mechanism of this epigenetic regulation. Herein, we developed a chemical proteomic approach, relying upon multivalent photoaffinity probes to capture binders of the mark, and identified ENL as a novel target of H3K9bhb. Biochemical studies and CUT&Tag analysis further suggested that ENL favorably binds to H3K9bhb, and co-localizes with it on promoter regions to modulate gene expression. Notably, disrupting the interaction between H3K9bhb and ENL via structure-based mutation led to the suppressed expression of genes such MYC that drive cell proliferation. Together, our work offered a chemoproteomics approach and identified ENL as a novel histone β-hydroxybutyrylation effector that regulates gene transcription, providing new insight into the regulation mechanism and function of histone Kbhb.
Collapse
Affiliation(s)
- Chen Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Cong Chen
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Aiyuan Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zixin Jiang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Fei Zhao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yanan Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yue Han
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Ziping Niu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Shanshan Tian
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
- Tianjin Key Laboratory of Digestive Diseases, Department of Gastroenterology and Hepatology, Medical University General Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Guijin Zhai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
2
|
Wan C, Yang D, Song C, Liang M, An Y, Lian C, Dai C, Ye Y, Yin F, Wang R, Li Z. A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells. Chem Sci 2024; 15:5340-5348. [PMID: 38577373 PMCID: PMC10988577 DOI: 10.1039/d3sc05766f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024] Open
Abstract
Protein active states are dynamically regulated by various modifications; thus, endogenous protein modification is an important tool for understanding protein functions and networks in complicated biological systems. Here we developed a new pyridinium-based approach to label lysine residues under physiological conditions that is low-toxicity, efficient, and lysine-selective. Furthermore, we performed a large-scale analysis of the ∼70% lysine-selective proteome in MCF-7 cells using activity-based protein profiling (ABPP). We quantifically assessed 1216 lysine-labeled peptides in cell lysates and identified 386 modified lysine sites including 43 mitochondrial-localized proteins in live MCF-7 cells. Labeled proteins significantly preferred the mitochondria. This pyridinium-based methodology demonstrates the importance of analyzing endogenous proteins under native conditions and provides a robust chemical strategy utilizing either lysine-selective protein labeling or spatiotemporal profiling in a living system.
Collapse
Affiliation(s)
- Chuan Wan
- College of Health Science and Environmental Engineering, Shenzhen Technology University Shenzhen 518118 P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering Guangzhou 510225 P. R. China
| | - Chunli Song
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Yuxin Ye
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| |
Collapse
|
3
|
Xie H, Zhang C. Potential of the nanoplatform and PROTAC interface to achieve targeted protein degradation through the Ubiquitin-Proteasome system. Eur J Med Chem 2024; 267:116168. [PMID: 38310686 DOI: 10.1016/j.ejmech.2024.116168] [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: 11/03/2023] [Revised: 01/11/2024] [Accepted: 01/21/2024] [Indexed: 02/06/2024]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system (UPS) plays a crucial role in selectively breaking down specific proteins. The ability of the UPS to target proteins effectively and expedite their removal has significantly contributed to the evolution of UPS-based targeted protein degradation (TPD) strategies. In particular, proteolysis targeting chimeras (PROTACs) are an immensely promising tool due to their high efficiency, extensive target range, and negligible drug resistance. This breakthrough has overcome the limitations posed by traditionally "non-druggable" proteins. However, their high molecular weight and constrained solubility impede the delivery of PROTACs. Fortunately, the field of nanomedicine has experienced significant growth, enabling the delivery of PROTACs through nanoscale drug-delivery systems, which effectively improves the stability, solubility, drug distribution, tissue-specific accumulation, and stimulus-responsive release of PROTACs. This article reviews the mechanism of action attributed to PROTACs and their potential implications for clinical applications. Moreover, we present strategies involving nanoplatforms for the effective delivery of PROTACs and evaluate recent advances in targeting nanoplatforms to the UPS. Ultimately, an assessment is conducted to determine the feasibility of utilizing PROTACs and nanoplatforms for UPS-based TPD. The primary aim of this review is to provide innovative, reliable solutions to overcome the current challenges obstructing the effective use of PROTACs in the management of cancer, neurodegenerative diseases, and metabolic syndrome. Therefore, this is a promising technology for improving the treatment status of major diseases.
Collapse
Affiliation(s)
- Hanshu Xie
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, China
| | - Chao Zhang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, China.
| |
Collapse
|
4
|
Fu JY, Huang SJ, Wang BL, Yin JH, Chen CY, Xu JB, Chen YL, Xu S, Dong T, Zhou HN, Ma XY, Pu YP, Li H, Yang XJ, Xie LS, Wang ZJ, Luo Q, Shao YX, Ye L, Zong ZR, Wei XD, Xiao WW, Niu ST, Liu YM, Xu HP, Yu CQ, Duan SZ, Zheng LY. Lysine acetyltransferase 6A maintains CD4 + T cell response via epigenetic reprogramming of glucose metabolism in autoimmunity. Cell Metab 2024; 36:557-574.e10. [PMID: 38237601 DOI: 10.1016/j.cmet.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Augmented CD4+ T cell response in autoimmunity is characterized by extensive metabolic reprogramming. However, the epigenetic molecule that drives the metabolic adaptation of CD4+ T cells remains largely unknown. Here, we show that lysine acetyltransferase 6A (KAT6A), an epigenetic modulator that is clinically associated with autoimmunity, orchestrates the metabolic reprogramming of glucose in CD4+ T cells. KAT6A is required for the proliferation and differentiation of proinflammatory CD4+ T cell subsets in vitro, and mice with KAT6A-deficient CD4+ T cells are less susceptible to experimental autoimmune encephalomyelitis and colitis. Mechanistically, KAT6A orchestrates the abundance of histone acetylation at the chromatin where several glycolytic genes are located, thus affecting glucose metabolic reprogramming and subsequent CD4+ T cell responses. Treatment with KAT6A small-molecule inhibitors in mouse models shows high therapeutic value for targeting KAT6A in autoimmunity. Our study provides novel insights into the epigenetic programming of immunometabolism and suggests potential therapeutic targets for patients with autoimmunity.
Collapse
Affiliation(s)
- Jia-Yao Fu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Shi-Jia Huang
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Bao-Li Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Jun-Hao Yin
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Chang-Yu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Jia-Bao Xu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yan-Lin Chen
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Department of Neurosurgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Shuo Xu
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310000, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Ting Dong
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Hao-Nan Zhou
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Xin-Yi Ma
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yi-Ping Pu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Hui Li
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Xiu-Juan Yang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Li-Song Xie
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Zhi-Jun Wang
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Qi Luo
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yan-Xiong Shao
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Lei Ye
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Zi-Rui Zong
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Xin-Di Wei
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Wan-Wen Xiao
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China
| | - Shu-Tong Niu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Yi-Ming Liu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - He-Ping Xu
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Science, Westlake University, Hangzhou 310024, China
| | - Chuang-Qi Yu
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiota and Systematic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200120, China; Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310000, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China.
| | - Ling-Yan Zheng
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200001, China; National Center for Stomatology & National Clinical Research Center of Oral Disease, Shanghai Key Laboratory of Stomatology, Shanghai 200001, China.
| |
Collapse
|
5
|
Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [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: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
Collapse
Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
6
|
Fan Z, Liu Z, Zhang N, Wei W, Cheng K, Sun H, Hao Q. Identification of SIRT3 as an eraser of H4K16la. iScience 2023; 26:107757. [PMID: 37720100 PMCID: PMC10504495 DOI: 10.1016/j.isci.2023.107757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/24/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023] Open
Abstract
Lysine lactylation (Kla) is a novel histone post-translational modification discovered in late 2019. Later, HDAC1-3, were identified as the robust Kla erasers. While the Sirtuin family proteins showed weak eraser activities toward Kla, as reported. However, the catalytic mechanisms and physiological functions of HDACs and Sirtuins are not identical. In this study, we observed that SIRT3 exhibits a higher eraser activity against the H4K16la site than the other human Sirtuins. Crystal structures revealed the detailed binding mechanisms between lactyl-lysine peptides and SIRT3. Furthermore, a chemical probe, p-H4K16laAlk, was developed to capture potential Kla erasers from cell lysates. SIRT3 was captured by this probe and detected via proteomic analysis. And another chemical probe, p-H4K16la-NBD, was developed to detect the eraser-Kla delactylation processes directly via fluorescence indication. Our findings and chemical probes provide new directions for further investigating Kla and its roles in gene transcription regulation.
Collapse
Affiliation(s)
- Zhuming Fan
- Institute of High Energy Physics, CAS, Beijing 100000, China
- Spallation Neutron Source Science Center, CAS, Dongguan, Guangdong 523000, China
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Zhiyang Liu
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Nan Zhang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Wenyu Wei
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Ke Cheng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Quan Hao
- Institute of High Energy Physics, CAS, Beijing 100000, China
- Spallation Neutron Source Science Center, CAS, Dongguan, Guangdong 523000, China
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
7
|
Zhu L, Hu S, Yan X, Zeng Q, Zhang B, Jiang L, Yao SQ, Ge J. Ugi reaction-assisted assembly of covalent PROTACs against glutathione peroxidase 4. Bioorg Chem 2023; 134:106461. [PMID: 36924654 DOI: 10.1016/j.bioorg.2023.106461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/06/2022] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Inducing cell ferroptosis by inactivating glutathione peroxidase 4 (GPX4) is a popular cancer treatment strategy. However, only few GPX4 inhibitors have been developed to date. PROteolysis Targeting Chimera (PROTAC) is a promising approach to provide new opportunities to overcome limitations of traditional therapeutics. Herein, a PROTAC-like activity-based probe PD-Q2 was first assembled using Ugi reaction, consisting of a known GPX4 inhibitor ML-162 homolog to the E3 ligase cereblon ligand-pomalidomide. Pull-down and immunoblotting analysis revealed that GPX4 was a covalent target of PD-Q2, but the degradation efficiency was weak. Therefore, a series of degraders was further synthesized by varying the linkers of heterofunctional PROTACs. Among these degraders, PD-4 and PD-P2 were found to promote effective GPX4 degradation via the ubiquitin-proteasome system and cause lipid ROS accumulation. PD-4 and PD-P2 showed potent inhibitory of colony formation and cell growth. Furthermore, we found that with pomalidomide, the degraders exhibit a high fluorescent signal that is mostly localized in the lysosome, which may affect the effectiveness of anti-cell proliferation. Overall, we provide GPX4 degraders for further exploring therapeutic potential of regulating ferroptosis.
Collapse
Affiliation(s)
- Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shiqi Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Qian Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Linye Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117544, Singapore.
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
| |
Collapse
|
8
|
Tantipanjaporn A, Wong MK. Development and Recent Advances in Lysine and N-Terminal Bioconjugation for Peptides and Proteins. Molecules 2023; 28:molecules28031083. [PMID: 36770752 PMCID: PMC9953373 DOI: 10.3390/molecules28031083] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
The demand for creation of protein diversity and regulation of protein function through native protein modification and post-translational modification has ignited the development of selective chemical modification methods for peptides and proteins. Chemical bioconjugation offers selective functionalization providing bioconjugates with desired properties and functions for diverse applications in chemical biology, medicine, and biomaterials. The amino group existing at the lysine residue and N-terminus of peptides and proteins has been extensively studied in bioconjugation because of its good nucleophilicity and high surface exposure. Herein, we review the development of chemical methods for modification of the amino groups on lysine residue and N-terminus featuring excellent selectivity, mild reaction conditions, short reaction time, high conversion, biocompatibility, and preservation of protein integrity. This review is organized based on the chemoselectivity and site-selectivity of the chemical bioconjugation reagents to the amino acid residues aiming to provide guidance for the selection of appropriate bioconjugation methods.
Collapse
|
9
|
Fiorentino F, Castiello C, Mai A, Rotili D. Therapeutic Potential and Activity Modulation of the Protein Lysine Deacylase Sirtuin 5. J Med Chem 2022; 65:9580-9606. [PMID: 35802779 PMCID: PMC9340778 DOI: 10.1021/acs.jmedchem.2c00687] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sirtiun 5 (SIRT5) is a NAD+-dependent protein lysine deacylase primarily located in mitochondria. SIRT5 displays an affinity for negatively charged acyl groups and mainly catalyzes lysine deglutarylation, desuccinylation, and demalonylation while possessing weak deacetylase activity. SIRT5 substrates play crucial roles in metabolism and reactive oxygen species (ROS) detoxification, and SIRT5 activity is protective in neuronal and cardiac physiology. Moreover, SIRT5 exhibits a dichotomous role in cancer, acting as context-dependent tumor promoter or suppressor. Given its multifaceted activity, SIRT5 is a promising target in the design of activators or inhibitors that might act as therapeutics in many pathologies, including cancer, cardiovascular disorders, and neurodegeneration. To date, few cellular-active peptide-based SIRT5 inhibitors (SIRT5i) have been described, and potent and selective small-molecule SIRT5i have yet to be discovered. In this perspective, we provide an outline of SIRT5's roles in different biological settings and describe SIRT5 modulators in terms of their mode of action, pharmacological activity, and structure-activity relationships.
Collapse
Affiliation(s)
- Francesco Fiorentino
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, Piazzala Aldo Moro 5, Rome 00185, Italy
| | - Carola Castiello
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, Piazzala Aldo Moro 5, Rome 00185, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, Piazzala Aldo Moro 5, Rome 00185, Italy
- Pasteur
Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzala Aldo Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, Piazzala Aldo Moro 5, Rome 00185, Italy
| |
Collapse
|