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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: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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2
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Overview of SIRT5 as a potential therapeutic target: Structure, function and inhibitors. Eur J Med Chem 2022; 236:114363. [DOI: 10.1016/j.ejmech.2022.114363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 01/21/2023]
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3
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Rajabi N, Hansen TN, Nielsen AL, Nguyen HT, Baek M, Bolding JE, Bahlke OØ, Petersen SEG, Bartling CRO, Strømgaard K, Olsen CA. Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme. Angew Chem Int Ed Engl 2022; 61:e202115805. [PMID: 35299278 PMCID: PMC9315039 DOI: 10.1002/anie.202115805] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 01/01/2023]
Abstract
Sirtuin 5 (SIRT5) is a protein lysine deacylase enzyme that regulates diverse biology by hydrolyzing ϵ-N-carboxyacyllysine posttranslational modifications in the cell. Inhibition of SIRT5 has been linked to potential treatment of several cancers but potent compounds with activity in cells have been lacking. Here we developed mechanism-based inhibitors that incorporate isosteres of a carboxylic acid residue that is important for high-affinity binding to the enzyme active site. By masking of the tetrazole moiety of the most potent candidate from our initial SAR study, we achieved potent and cytoselective growth inhibition for the treatment of SIRT5-dependent leukemic cancer cell lines in culture. Thus, we provide an efficient, cellularly active small molecule that targets SIRT5, which can help elucidate its function and potential as a future drug target. This work shows that masked isosteres of carboxylic acids are viable chemical motifs for the development of inhibitors that target mitochondrial enzymes, which may have applications beyond the sirtuin field.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Present address: Red Glead Discovery, 22363, Lund, Sweden
| | - Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Present address: Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Huy T Nguyen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Present address: School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael Baek
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Julie E Bolding
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Oskar Ø Bahlke
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Sylvester E G Petersen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Christian R O Bartling
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
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4
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Rajabi N, Hansen TN, Nielsen AL, Nguyen HT, Bæk M, Bolding JE, Bahlke OØ, Petersen SEG, Bartling CR, Strømgaard K, Olsen CA. Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115805] [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)
- Nima Rajabi
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Tobias N. Hansen
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Alexander L. Nielsen
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Huy T. Nguyen
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Michael Bæk
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Julie. E. Bolding
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Oskar Ø. Bahlke
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Sylvester E. G. Petersen
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Christian R.O. Bartling
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Kristian Strømgaard
- Københavns Universitet: Kobenhavns Universitet Department of Drug Design and Pharmacology DENMARK
| | - Christian Adam Olsen
- University of Copenhagen Center for Biopharmaceuticals Universitetsparken 2 DK-2100 Copenhagen DENMARK
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5
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Marina Auth
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kathrin R. Troelsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Martin Pannek
- Universität Bayreuth; Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Dhaval P. Bhatt
- Duke University Medical Center; Sarah W. Stedman Nutrition and Metabolism Center; 4321 Medical Park Drive Durham NC 27704 USA
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Matthew D. Hirschey
- Duke University Medical Center; Sarah W. Stedman Nutrition and Metabolism Center; 4321 Medical Park Drive Durham NC 27704 USA
| | - Clemens Steegborn
- Universität Bayreuth; Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Andreas S. Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew Chem Int Ed Engl 2017; 56:14836-14841. [PMID: 29044784 PMCID: PMC5814306 DOI: 10.1002/anie.201709050] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Indexed: 12/18/2022]
Abstract
The sirtuin enzymes are important regulatory deacylases in a variety of biochemical contexts and may therefore be potential therapeutic targets through either activation or inhibition by small molecules. Here, we describe the discovery of the most potent inhibitor of sirtuin 5 (SIRT5) reported to date. We provide rationalization of the mode of binding by solving co-crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more "drug-like" properties. Importantly, enzyme kinetic evaluation revealed a slow, tight-binding mechanism of inhibition, which is unprecedented for SIRT5. This is important information when applying inhibitors to probe mechanisms in biology.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Marina Auth
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kathrin R Troelsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Martin Pannek
- Universität Bayreuth, Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Dhaval P Bhatt
- Duke University Medical Center, Sarah W. Stedman Nutrition and Metabolism Center, 4321 Medical Park Drive, Durham, NC, 27704, USA
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Matthew D Hirschey
- Duke University Medical Center, Sarah W. Stedman Nutrition and Metabolism Center, 4321 Medical Park Drive, Durham, NC, 27704, USA
| | - Clemens Steegborn
- Universität Bayreuth, Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
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Simic Z, Weiwad M, Schierhorn A, Steegborn C, Schutkowski M. The ɛ-Amino Group of Protein Lysine Residues Is Highly Susceptible to Nonenzymatic Acylation by Several Physiological Acyl-CoA Thioesters. Chembiochem 2015; 16:2337-47. [PMID: 26382620 DOI: 10.1002/cbic.201500364] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 01/04/2023]
Abstract
Mitochondrial enzymes implicated in the pathophysiology of diabetes, cancer, and metabolic syndrome are highly regulated by acetylation. However, mitochondrial acetyltransferases have not been identified. Here, we show that acetylation and also other acylations are spontaneous processes that depend on pH value, acyl-CoA concentration and the chemical nature of the acyl residue. In the case of a peptide derived from carbamoyl phosphate synthetase 1, the rates of succinylation and glutarylation were up to 150 times than for acetylation. These results were confirmed by using the protein substrate cyclophilin A (CypA). Deacylation experiments revealed that SIRT3 exhibits deacetylase activity but is not able to remove any of the succinyl groups from CypA, whereas SIRT5 is an effective protein desuccinylase. Thus, the acylation landscape on lysine residues might largely depend on the enzymatic activity of specific sirtuins, and the availability and reactivity of acyl-CoA compounds.
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Affiliation(s)
- Zeljko Simic
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Matthias Weiwad
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany
| | - Clemens Steegborn
- Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120, Halle, Germany.
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