1
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Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem 2024; 16:913-921. [PMID: 38531969 DOI: 10.1038/s41557-024-01500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to -1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein-DNA and protein-protein interactions in biological processes from replication to ubiquitin signalling.
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Affiliation(s)
- Maria Weyh
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marie-Lena Jokisch
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tuan-Anh Nguyen
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maximilian Fottner
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Kathrin Lang
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany.
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2
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Hansen T, Danková D, Bæk M, Grlaš L, Olsen CA. Sulfur(VI) Fluoride Exchange Chemistry in Solid-Phase Synthesis of Compound Arrays: Discovery of Histone Deacetylase Inhibitors. JACS AU 2024; 4:1854-1862. [PMID: 38818074 PMCID: PMC11134391 DOI: 10.1021/jacsau.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/01/2024]
Abstract
Multistep synthesis performed on solid support is a powerful means to generate small-molecule libraries for the discovery of chemical probes to dissect biological mechanisms as well as for drug discovery. Therefore, expansion of the collection of robust chemical transformations amenable to solid-phase synthesis is desirable for achieving chemically diverse libraries for biological testing. Here, we show that sulfur(VI) fluoride exchange (SuFEx) chemistry, exemplified by pairing phenols with aryl fluorosulfates, can be used for the solid-phase synthesis of biologically active compounds. As a case study, we designed and synthesized a library of 84 hydroxamic acid-containing small molecules, providing a rich source of inhibitors with diverse selectivity profiles across the human histone deacetylase enzyme family. Among other discoveries, we identified a scaffold that furnished inhibitors of HDAC11 with exquisite selectivity in vitro and a selective inhibitor of HDAC6 that was shown to affect the acetylation of α-tubulin over histone sites H3K18, H3K27, as well as SMC3 in cultured cells. Our results encourage the further use of SuFEx chemistry for the synthesis of diverse small-molecule libraries and provide insight for future design of selective HDAC inhibitors.
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Affiliation(s)
| | | | | | - Linda Grlaš
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
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3
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Bursch KL, Goetz CJ, Smith BC. Current Trends in Sirtuin Activator and Inhibitor Development. Molecules 2024; 29:1185. [PMID: 38474697 DOI: 10.3390/molecules29051185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Sirtuins are NAD+-dependent protein deacylases and key metabolic regulators, coupling the cellular energy state with selective lysine deacylation to regulate many downstream cellular processes. Humans encode seven sirtuin isoforms (Sirt1-7) with diverse subcellular localization and deacylase targets. Sirtuins are considered protective anti-aging proteins since increased sirtuin activity is canonically associated with lifespan extension and decreased activity with developing aging-related diseases. However, sirtuins can also assume detrimental cellular roles where increased activity contributes to pathophysiology. Modulation of sirtuin activity by activators and inhibitors thus holds substantial potential for defining the cellular roles of sirtuins in health and disease and developing therapeutics. Instead of being comprehensive, this review discusses the well-characterized sirtuin activators and inhibitors available to date, particularly those with demonstrated selectivity, potency, and cellular activity. This review also provides recommendations regarding the best-in-class sirtuin activators and inhibitors for practical research as sirtuin modulator discovery and refinement evolve.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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4
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Wang J, Zhang S, Li Y, Xu Q, Kritzer JA. Investigating the Cytosolic Delivery of Proteins by Lipid Nanoparticles Using the Chloroalkane Penetration Assay. Biochemistry 2024. [PMID: 38334719 DOI: 10.1021/acs.biochem.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Protein therapeutics are an expanding area for research and drug development, and lipid nanoparticles (LNPs) are the most prominent nonviral vehicles for protein delivery. The most common methods for assessing protein delivery by LNPs include assays that measure the total amount of protein taken up by cells and assays that measure the phenotypic changes associated with protein delivery. However, assays for total cellular uptake include large amounts of protein that are trapped in endosomes or are otherwise nonfunctional. Assays for functional delivery are important, but the readouts are indirect and amplified, limiting the quantitative interpretation. Here, we apply an assay for cytosolic delivery, the chloroalkane penetration assay (CAPA), to measure the cytosolic delivery of a (-30) green fluorescent protein (GFP) fused to Cre recombinase (Cre(-30)GFP) fusion protein by LNPs. We compare these data to the data from total cellular uptake and functional delivery assays to provide a richer analysis of uptake and endosomal escape for LNP-mediated protein delivery. We also use CAPA for a screen of a small library of lipidoids, identifying those with a promising ability to deliver Cre(-30)GFP to the cytosol of mammalian cells. With careful controls and optimized conditions, we expect that CAPA will be a useful tool for investigating the rate, efficiency, and mechanisms of LNP-mediated delivery of therapeutic proteins.
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Affiliation(s)
- Jing Wang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Shiying Zhang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yamin Li
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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5
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Bolding JE, Nielsen AL, Jensen I, Hansen TN, Ryberg LA, Jameson ST, Harris P, Peters GHJ, Denu JM, Rogers JM, Olsen CA. Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7. Angew Chem Int Ed Engl 2023; 62:e202314597. [PMID: 37873919 DOI: 10.1002/anie.202314597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
The sirtuins are NAD+ -dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.
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Affiliation(s)
- Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
- Current address: Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Iben Jensen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Line A Ryberg
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Immunology and Microbiology, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Samuel T Jameson
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Current address: Department of Chemistry, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Joseph M Rogers
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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6
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Wang L, Hu L, Deng J, Hou S, Mou L, Lei P, Chen X, Liu J, Jiang Y, Xiong R, Tian X, Zhang W, Li R, Yang W, Yang L. Design, synthesis and biological evaluation of 2,4,6- trisubstituted triazine derivatives as new nonpeptide small-molecule SIRT5 inhibitors. Bioorg Med Chem 2023; 93:117455. [PMID: 37643500 DOI: 10.1016/j.bmc.2023.117455] [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: 06/30/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Human sirtuin 5 (SIRT5) participates in a variety of metabolic disorder-associated diseases, including cancer. Inhibition of SIRT5 has been confirmed to provide a new strategy for treatment of related diseases. Previously, we discovered a pyrimidine skeleton inhibitor XIV, which showed low micromolar inhibitory activity against SIRT5. Herein, we utilized the scaffold-hopping strategy to design and synthesize a series of 2,4,6- trisubstituted triazine derivatives. The SAR analysis led to the discovery of several new SIRT5 inhibitors with low micromolar inhibition levels. The most potent compounds 10 (IC50 = 5.38 µM), and 14 (IC50 = 4.07 µM) were further confirmed to be the substrate-competitive SIRT5 inhibitors through enzyme kinetic assays, which is consistent with the molecular docking analyses. Fluorescence-based thermal shift assays proved that these compounds may stabilize SIRT5 by binding withprotein.. In addition, compounds 10 and 14 were also revealed to have moderate selectivity to SIRT5 over SIRT1-3. This study will aid further efforts to develop highly potent and selective SIRT5 inhibitors for the treatment of cancer and other related diseases.
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Affiliation(s)
- Lijiao Wang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Lei Hu
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Jianlin Deng
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Suyan Hou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Luohe Mou
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Pengcheng Lei
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Xi Chen
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Jiayu Liu
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Yingying Jiang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Rui Xiong
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Xiangqin Tian
- Fuan Group Chongqing Kingsday Pharmaceutical Co., LTD, Chongqing 401120, China
| | - Weifeng Zhang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Rong Li
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Wenyu Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China.
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7
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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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8
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Fabbrizi E, Fiorentino F, Carafa V, Altucci L, Mai A, Rotili D. Emerging Roles of SIRT5 in Metabolism, Cancer, and SARS-CoV-2 Infection. Cells 2023; 12:cells12060852. [PMID: 36980194 PMCID: PMC10047932 DOI: 10.3390/cells12060852] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Sirtuin 5 (SIRT5) is a predominantly mitochondrial enzyme catalyzing the removal of glutaryl, succinyl, malonyl, and acetyl groups from lysine residues through a NAD+-dependent deacylase mechanism. SIRT5 is an important regulator of cellular homeostasis and modulates the activity of proteins involved in different metabolic pathways such as glycolysis, tricarboxylic acid (TCA) cycle, fatty acid oxidation, electron transport chain, generation of ketone bodies, nitrogenous waste management, and reactive oxygen species (ROS) detoxification. SIRT5 controls a wide range of aspects of myocardial energy metabolism and plays critical roles in heart physiology and stress responses. Moreover, SIRT5 has a protective function in the context of neurodegenerative diseases, while it acts as a context-dependent tumor promoter or suppressor. In addition, current research has demonstrated that SIRT5 is implicated in the SARS-CoV-2 infection, although opposing conclusions have been drawn in different studies. Here, we review the current knowledge on SIRT5 molecular actions under both healthy and diseased settings, as well as its functional effects on metabolic targets. Finally, we revise the potential of SIRT5 as a therapeutic target and provide an overview of the currently reported SIRT5 modulators, which include both activators and inhibitors.
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Affiliation(s)
- Emanuele Fabbrizi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, Università degli Studi della Campania “L. Vanvitelli”, 80138 Naples, Italy
- BIOGEM, 83031 Ariano Irpino, Italy
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania “L. Vanvitelli”, 80138 Naples, Italy
- BIOGEM, 83031 Ariano Irpino, Italy
- IEOS—Istituto per l’Endocrinologia e Oncologia Sperimentale, CNR, 80131 Naples, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
- Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.M.); (D.R.); Tel.: +39-0649913392 (A.M.); +39-0649913237 (D.R.); Fax: +39-0649693268 (A.M.)
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.M.); (D.R.); Tel.: +39-0649913392 (A.M.); +39-0649913237 (D.R.); Fax: +39-0649693268 (A.M.)
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9
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Yao J, Yin Y, Han H, Chen S, Zheng Y, Liang B, Wu M, Shu K, Debnath B, Lombard DB, Wang Q, Cheng K, Neamati N, Liu Y. Pyrazolone derivatives as potent and selective small-molecule SIRT5 inhibitors. Eur J Med Chem 2023; 247:115024. [PMID: 36543033 DOI: 10.1016/j.ejmech.2022.115024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Sirtiun 5 (SIRT5) is a NAD+-dependent protein lysine deacylase. It is emerging as a promising target for the development of drugs to treat cancer and metabolism-related diseases. In this study, we screened 5000 compounds and identified a hit compound 14 bearing a pyrazolone functional group as a novel SIRT5-selective inhibitor. Structure-based optimization of 14 resulted in compound 47 with an IC50 value of 0.21 ± 0.02 μM and a 100-fold improved potency. Compound 47 showed substantial selectivity for SIRT5 over SIRT1-3 and SIRT6. Biochemical studies suggest that 47 does not occupy the NAD + -binding pocket and acts as a substrate-competitive inhibitor. The identified potent and selective SIRT5 inhibitors allow further studies as research tools and therapeutic agents.
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Affiliation(s)
- Jian Yao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yudong Yin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Hong Han
- The First Affiliated Hospital of Dali University, Dali, 671000, PR China
| | - Shaoting Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yuxiang Zheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Benji Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Mengyue Wu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Kangqi Shu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States
| | - David B Lombard
- Department of Pathology & Laboratory Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, United States
| | - Quande Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Keguang Cheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States.
| | - Yanghan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
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10
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Bolding JE, Martín‐Gago P, Rajabi N, Gamon LF, Hansen TN, Bartling CRO, Strømgaard K, Davies MJ, Olsen CA. Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase. Angew Chem Int Ed Engl 2022; 61:e202204565. [PMID: 36130196 PMCID: PMC9828517 DOI: 10.1002/anie.202204565] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/12/2023]
Abstract
The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ-N-carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate-based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne-tagged affinity-labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.
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Affiliation(s)
- Julie E. Bolding
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Luke F. Gamon
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Tobias N. Hansen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Christian R. O. Bartling
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Michael J. Davies
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
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11
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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: 18] [Impact Index Per Article: 9.0] [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.
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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
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12
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Mori M, Cazzaniga G, Meneghetti F, Villa S, Gelain A. Insights on the Modulation of SIRT5 Activity: A Challenging Balance. Molecules 2022; 27:4449. [PMID: 35889322 PMCID: PMC9316768 DOI: 10.3390/molecules27144449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023] Open
Abstract
SIRT5 is a member of the Sirtuin family, a class of deacetylating enzymes consisting of seven isoforms, involved in the regulation of several processes, including gene expression, metabolism, stress response, and aging. Considering that the anomalous activity of SIRT5 is linked to many pathological conditions, we present herein an overview of the most interesting modulators, with the aim of contributing to further development in this field.
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Affiliation(s)
| | | | | | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (G.C.); (F.M.); (A.G.)
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13
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Bucci R, Vaghi F, Di Lorenzo D, Anastasi F, Broggini G, Lo Presti L, Contini A, Gelmi ML. A Non‐coded β2,2‐Amino Acid with Isoxazoline Core Able to Stabilize Peptides Folding Through an Unprecedented Hydrogen Bond. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Raffaella Bucci
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Vaghi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Davide Di Lorenzo
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Francesco Anastasi
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Gianluigi Broggini
- Università degli Studi dell'Insubria Dipartimento di Scienza e Alta Tecnologia ITALY
| | - Leonardo Lo Presti
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Chimica ITALY
| | - Alessandro Contini
- Università degli Studi di Milano: Universita degli Studi di Milano Dipartimento di Scienze Farmaceutiche ITALY
| | - Maria Luisa Gelmi
- Universita degli Studi di Milano DISFARM, Sezione di Chimica Generale e Organica “A. Marchesini” Via Venezian 21 20133 Milano ITALY
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