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Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
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Affiliation(s)
- 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
| | - 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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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Gless BH, Schmied SH, Bejder BS, Olsen CA. Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters in Biochemistry and Native Chemical Ligation. JACS Au 2023; 3:1443-1451. [PMID: 37234128 PMCID: PMC10207088 DOI: 10.1021/jacsau.3c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Thioesters are considered to be "energy-rich" functional groups that are susceptible to attack by thiolate and amine nucleophiles while remaining hydrolytically stable at neutral pH, which enables thioester chemistry to take place in an aqueous medium. Thus, the inherent reactivity of thioesters enables their fundamental roles in biology and unique applications in chemical synthesis. Here, we investigate the reactivity of thioesters that mimic acyl-coenzyme A (CoA) species and S-acylcysteine modifications as well as aryl thioesters applied in chemical protein synthesis by native chemical ligation (NCL). We developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles (hydroxide, thiolate, and amines) under various conditions and were able to recapitulate previously reported reactivity of thioesters. Further, chromatography-based analyses of acetyl- and succinyl-CoA mimics revealed striking differences in their ability to acylate lysine side chains, providing insight into nonenzymatic protein acylation. Finally, we investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol-thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight into the potential optimization of native chemical ligation chemistry.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
ConspectusThe sophistication of proteomic analysis has revealed that protein lysine residues are posttranslationally modified by a variety of acyl groups. Protein lysine acetylation regulates metabolism, gene expression, and microtubule formation and has been extensively studied; however, the understanding of the biological significance of other acyl posttranslational modifications (PTMs) is still in its infancy. The acylation of lysine residues is mediated either by acyltransferase "writer" enzymes or by nonenzymatic mechanisms and hydrolase enzymes, termed "erasers", that cleave various acyl PTMs to reverse the modified state. We have studied the human lysine deacylase enzymes, comprising the 11 Zn2+-dependent histone deacetylases (HDACs) and the 7 NAD+-consuming sirtuins (SIRTs), over the past decade. We have thus developed selective inhibitors and molecular probes and have studied the acyl substrate scope of each enzyme using chemically synthesized peptide substrates and photo-cross-linking probes. Recently, we have turned our attention to PTMs containing a stereogenic center, such as ε-N-β-hydroxybutyryllysine (Kbhb) and ε-N-lactyllysine (Kla), that each comprise a pair of mirror image stereoisomers as modifications. Both modifications are found on histones, where they affect gene transcription in response to specific metabolic states, and they are found on cytosolic and mitochondrial enzymes involved in fatty acid oxidation (Kbhb) and glycolysis (Kla), respectively. Thus, chiral modifications to lysine side chains give rise to two distinct diastereomeric products, with separate metabolic origins and potentially different activities exhibited by writer and eraser enzymes. Lysine l-lactylation originates from l-lactate, a major energy carrier produced from pyruvate after glycolysis, and it is highly induced by metabolic states such as the Warburg effect. l-Lactate can possibly be activated by acyl-coenzyme A (CoA) synthetases and transferred to lysine residues by histone acetyltransferases such as p300. d-Lactylation, on the other hand, arises primarily from a nonenzymatic reaction with d-lactylglutathione, an intermediate in the glyoxalase pathway. In addition to their distinct origin, we found that both K(l-la) and K(d-la) modifications are erased by HDACs with different catalytic efficiencies. Also, K(l-bhb) and K(d-bhb) arise from different metabolites but depend on interconnected metabolic pathways, and the two stereoisomers of ε-N-3-hydroxy-3-methylglutaryllysine (Khmg) originate from a single precursor that may then be regulated differently by eraser enzymes. Distinguishing between the individual stereoisomers of PTMs is therefore of crucial importance. In the present Account, we will (1) revisit the long-standing evidence for the distinct production and dynamics of enantiomeric forms of chiral metabolites that serve as ε-N-acyllysine PTMs and (2) highlight the outstanding questions that arise from the recent literature on chiral lysine PTMs resulting from these metabolites.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Fabrizio Monda
- Center for Biopharmaceuticals & Department of Drug Design of 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 of Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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7
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Moreno-Yruela C, Olsen CA. Determination of Slow-Binding HDAC Inhibitor Potency and Subclass Selectivity. ACS Med Chem Lett 2022; 13:779-785. [PMID: 35586419 PMCID: PMC9109163 DOI: 10.1021/acsmedchemlett.1c00702] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/10/2022] [Indexed: 12/27/2022] Open
Abstract
Histone deacetylases (HDACs) 1-3 regulate chromatin structure and gene expression. These three enzymes are targets for cancer chemotherapy and have been studied for the treatment of immune disorders and neurodegeneration, but there is a lack of selective pharmacological tool compounds to unravel their individual roles. Potent inhibitors of HDACs 1-3 often display slow-binding kinetics, which causes a delay in inhibitor-enzyme equilibration and may affect assay readout. Here we compare the potencies and selectivities of slow-binding inhibitors measured by discontinuous and continuous assays. We find that entinostat, a clinical candidate, inhibits HDACs 1-3 by a two-step slow-binding mechanism with lower potencies than previously reported. In addition, we show that RGFP966, commercialized as an HDAC3-selective probe, is a slow-binding inhibitor with inhibitor constants of 57, 31, and 13 nM against HDACs 1-3, respectively. These data highlight the need for thorough kinetic investigation in the development of selective HDAC probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 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, DK-2100 Copenhagen, Denmark
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8
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Moreno-Yruela C, Zhang D, Wei W, Bæk M, Liu W, Gao J, Danková D, Nielsen AL, Bolding JE, Yang L, Jameson ST, Wong J, Olsen CA, Zhao Y. Class I histone deacetylases (HDAC1-3) are histone lysine delactylases. Sci Adv 2022; 8:eabi6696. [PMID: 35044827 PMCID: PMC8769552 DOI: 10.1126/sciadv.abi6696] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/25/2021] [Indexed: 05/22/2023]
Abstract
Lysine L-lactylation [K(L-la)] is a newly discovered histone mark stimulated under conditions of high glycolysis, such as the Warburg effect. K(L-la) is associated with functions that are different from the widely studied histone acetylation. While K(L-la) can be introduced by the acetyltransferase p300, histone delactylases enzymes remained unknown. Here, we report the systematic evaluation of zinc- and nicotinamide adenine dinucleotide–dependent histone deacetylases (HDACs) for their ability to cleave ε-N-L-lactyllysine marks. Our screens identified HDAC1–3 and SIRT1–3 as delactylases in vitro. HDAC1–3 show robust activity toward not only K(L-la) but also K(D-la) and diverse short-chain acyl modifications. We further confirmed the de-L-lactylase activity of HDACs 1 and 3 in cells. Together, these data suggest that histone lactylation is installed and removed by regulatory enzymes as opposed to spontaneous chemical reactivity. Our results therefore represent an important step toward full characterization of this pathway’s regulatory elements.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Di Zhang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Michael Bæk
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Wenchao Liu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jinjun Gao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Daniela Danková
- Center for Biopharmaceuticals and 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 and 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 and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lu Yang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Samuel T. Jameson
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Christian A. Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Corresponding author. (Y.Z.); (C.A.O.)
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
- Corresponding author. (Y.Z.); (C.A.O.)
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9
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Gless BH, Olsen CA. On-Resin Peptide Cyclization Using the 3-Amino-4-(Methylamino)Benzoic Acid MeDbz Linker. Methods Mol Biol 2022; 2371:101-115. [PMID: 34596845 DOI: 10.1007/978-1-0716-1689-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cyclic peptides are becoming increasingly important in drug discovery due to their specific binding properties, larger surface area compared to small molecules, and their ready and modular synthetic accessibility. In this protocol, we describe an on-resin, cleavage-inducing cyclization methodology for the synthesis of cyclic thiodepsipeptides and cyclic homodetic peptides using the 3-amino-4-(methylamino)benzoic acid (MeDbz) linker. We further describe three post-cyclization one-pot procedures, which include desulfurization, disulfide bond formation, and S-alkylation of cysteine residues.
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Affiliation(s)
- Bengt H Gless
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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10
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Gless BH, Bejder BS, Monda F, Bojer MS, Ingmer H, Olsen CA. Rearrangement of Thiodepsipeptides by S → N Acyl Shift Delivers Homodetic Autoinducing Peptides. J Am Chem Soc 2021; 143:10514-10518. [PMID: 34228933 DOI: 10.1021/jacs.1c02614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Group behavior in many bacteria relies on chemically induced communication called quorum sensing (QS), which plays important roles in the regulation of colonization, biofilm formation, and virulence. In Gram-positive bacteria, QS is often mediated by cyclic ribosomally synthesized and posttranslationally modified peptides (RiPPs). In staphylococci, for example, most of these so-called autoinducing peptides (AIPs) contain a conserved thiolactone functionality, which has also been predicted to constitute a structural feature of AIPs from other genera. Here, we show that pentameric AIPs from Lactiplantibacillus plantarum, Clostridium perfringens, and Listeria monocytogenes that were previously presumed to be thiolactone-containing structures readily rearrange to become homodetic cyclopeptides. This finding has implications for the developing understanding of cross-species and potential cross-genus communication of bacteria and may help guide the discovery of peptide ligands to perturb their function.
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Affiliation(s)
- Bengt H Gless
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Benjamin S Bejder
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Fabrizio Monda
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Martin S Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and 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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11
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Yan D, Franzini A, Pomicter AD, Halverson BJ, Antelope O, Mason CC, Ahmann JM, Senina AV, Jones CLL, Zabriskie MS, Than H, Xiao MJ, van Scoyk A, Patel AB, Heaton WLL, Owen SC, Andersen JL, Egbert CM, Reisz JA, D'Alessandro A, Cox JE, Gantz KC, Redwine HM, Iyer SM, Khorashad JS, Rajabi N, Olsen CA, O'Hare T, Deininger MW. Abstract LB109: A critical role for SIRT5 in acute myeloid leukemia metabolism. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Standard of care for AML includes chemotherapy and stem cell transplant, with 5-year survival rates <30%. We sought to identify genes critical to AML cells, irrespective of mutational status, and performed an shRNA screen targeting 1,287 genes on 12 AML patient samples. This screen identified Sirtuin 5 (SIRT5) as a top candidate. SIRT5 is the only known enzyme with desuccinylase, demalonylase, and/or deglutarylase activity and we are the first to report the dependence of AML cells on SIRT5. Next, we stably transduced a panel of AML cell lines with doxycycline (dox)-inducible shSIRT5 (dox-shSIRT5). SIRT5 knockdown (KD) strongly inhibited cell growth, colony formation and increased apoptosis in 15/22 lines (SIRT5-dependent), while 7/22 lines were SIRT5-independent. SIRT5 dependence did not correlate with AML-related mutations nor basal SIRT5 expression. SIRT5 KD in primary AML samples (N=25) revealed a therapeutic window (~50% reduction), with no effect in CB samples (N=5). We examined the requirement of SIRT5 in vivo using three mouse models of leukemia. In a xenograft model with AML cell lines, SIRT5 KD indefinitely prolonged survival of mice injected with SIRT5-dependent cells with no sign of leukemia. Bone marrow transplant with transduced (MLL-AF9 or BCR-ABL1) SIRT5 null cells showed reduced leukemia cell burden and splenomegaly, and significantly prolonged survival. FLT3-ITD-driven disease was also blunted by the absence of SIRT5 in a genetic knockout mouse model. Mechanically, SIRT5 KD profoundly reduced oxidative phosphorylation (OXPHOS) and glycolysis. Additionally, SIRT5 KD increased mitochondrial superoxide selectively in annexin V-negative, SIRT5-dependent cells. Concomitant, ectopic expression of SOD2 abrogated the increase in superoxide, rescued cells from apoptosis, and rescued the colony formation deficit. Untargeted metabolomics revealed RNA charging and alanine and serine metabolism as top metabolic pathways regulated by SIRT5, with glutaminase (GLS) and α-ketoglutarate identified as potential upstream regulators. Metabolic tracing experiments with [13C5,15N2]-glutamine confirmed disrupted glutamine metabolism in SIRT5-dependent cells. Together, these results indicate that SIRT5 is required to regulate glutamine flux to sustain redox homeostasis and/or anabolism. NRD167, a novel SIRT5 inhibitor, was used to target SIRT5 in AML. NRD167 reduced cell proliferation, induced apoptosis, and reduced OXPHOS in SIRT5-dependent but not SIRT5-independent cells. NRD167 inhibited colony formation from AML patient samples, but not in CB samples. An AML patient-derived xenograft model trended toward prolonged survival following ex vivo treatment with NRD167. Our data suggest that the majority of AML samples are dependent on SIRT5 and that inhibition preferentially targets AML cells, implicating SIRT5 as a therapy target in AML.
Citation Format: Dongqing Yan, Anca Franzini, Anthony D. Pomicter, Brayden J. Halverson, Orlando Antelope, Clinton C. Mason, Jonathan M. Ahmann, Anna V. Senina, Courtney L. L. Jones, Matthew S. Zabriskie, Hein Than, Michael J. Xiao, Alexandria van Scoyk, Ami B. Patel, William L. L. Heaton, Shawn C. Owen, Joshua L. Andersen, Christina M. Egbert, Julie A. Reisz, Angelo D'Alessandro, James E. Cox, Kevin C. Gantz, Hannah M. Redwine, Siddharth M. Iyer, Jamshid S. Khorashad, Nima Rajabi, Christian A. Olsen, Thomas O'Hare, Michael W. Deininger. A critical role for SIRT5 in acute myeloid leukemia metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB109.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Hein Than
- 1University of Utah, Salt Lake City, UT
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nima Rajabi
- 5University of Copenhagen, Copenhagen, Denmark
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12
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Yruela I, Moreno-Yruela C, Olsen CA. Zn 2+-Dependent Histone Deacetylases in Plants: Structure and Evolution. Trends Plant Sci 2021; 26:741-757. [PMID: 33461867 DOI: 10.1016/j.tplants.2020.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Zn2+-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain; Group of Biochemistry, Biophysics, and Computational Biology (GBsC), Institute for Biocomputation and Physics of Complex Systems (BIFI) and Universidad de Zaragoza (UNIZAR) Joint Unit to CSIC, Zaragoza, Spain.
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 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, Universitetsparken 2, 2100 Copenhagen, Denmark
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13
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Troelsen KS, Bæk M, Nielsen AL, Madsen AS, Rajabi N, Olsen CA. Mitochondria-targeted inhibitors of the human SIRT3 lysine deacetylase. RSC Chem Biol 2021; 2:627-635. [PMID: 34458804 PMCID: PMC8341665 DOI: 10.1039/d0cb00216j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/24/2021] [Indexed: 11/21/2022] Open
Abstract
Sirtuin 3 (SIRT3) is the major protein lysine deacetylase in the mitochondria. This hydrolase regulates a wide range of metabolically involved enzymes and has been considered as a potential drug target in certain cancers. Investigation of pharmacological intervention has been challenging due to a lack of potent and selective inhibitors of SIRT3. Here, we developed a strategy for selective inhibition of SIRT3 in cells, over its structurally similar isozymes that localize primarily to the nucleus (SIRT1) and the cytosol (SIRT2). This was achieved by directing the inhibitors to the mitochondria through incorporation of mitochondria-targeting peptide sequences into the inhibitor structures. Our inhibitors exhibited excellent mitochondrial localization in HeLa cells as indicated by fluorophore-conjugated versions, and target engagement was demonstrated by a cellular thermal shift assay of SIRT3 using western blotting. The acetylation state of documented SIRT3 target MnSOD was shown to be increased in cells with little effect on known targets of SIRT1 and SIRT2, showing that our lead compound exhibits selectivity for SIRT3 in cells. We expect that the developed inhibitor will now enable a more detailed investigation of SIRT3 as a potential drug target and help shed further light on the diverse biology regulated by this enzyme.
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Affiliation(s)
- Kathrin S Troelsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Michael Bæk
- 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
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - 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
| | - 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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14
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Abstract
Histone deacetylases (HDACs) are ubiquitous enzymes that cleave post-translational ε-N-acyllysine modifications. The continued identification of diverse acyl modifications at lysine residues in proteins has resulted in discovery of new insight into the biological roles of these enzymes. Here, we describe a fluorogenic high-throughput screening protocol to identify deacylase activities. We describe the careful optimization of continuous, coupled enzyme assays, which provide efficient determination of kinetic parameters. These techniques can facilitate inhibitor assay design and provide fundamental understanding of HDAC biochemistry. For complete details on the use and execution of this protocol, please refer to Moreno-Yruela et al. (2018). Histone deacetylases hydrolyze multiple different acyl modifications of lysine Fluorogenic substrates enable high-throughput screening of deacylase activities We develop continuous, coupled enzyme assays by careful optimization Continuous assays allow accurate determination of enzyme kinetic parameters
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 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, Universitetsparken 2, 2100 Copenhagen, Denmark
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15
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Nielsen AL, Rajabi N, Kudo N, Lundø K, Moreno-Yruela C, Bæk M, Fontenas M, Lucidi A, Madsen AS, Yoshida M, Olsen CA. Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration. RSC Chem Biol 2021; 2:612-626. [PMID: 34458803 PMCID: PMC8341974 DOI: 10.1039/d0cb00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme. Here, we report a collection of chemical probes that are potent, selective, stable in serum, water-soluble, and inhibit SIRT2-mediated deacetylation and demyristoylation in cells. Compared to the current landscape of SIRT2 inhibitors, this is a unique ensemble of features built into a single compound. We expect the developed chemotypes to find broad application in the interrogation of SIRT2 functions in both healthy and diseased cells, and to provide a foundation for the development of future therapeutics. Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. Here, we developed small peptide-based inhibitors of its activity in living cells in culture.![]()
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Affiliation(s)
- 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
| | - 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
| | - Norio Kudo
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Kathrine Lundø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B DK-2200 Copenhagen Denmark
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Alessia Lucidi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - 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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16
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Moreno-Yruela C, Bæk M, Vrsanova AE, Schulte C, Maric HM, Olsen CA. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat Commun 2021; 12:62. [PMID: 33397936 PMCID: PMC7782793 DOI: 10.1038/s41467-020-20250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Adela-Eugenie Vrsanova
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Institute of Applied Biosciences & Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, D-76131, Karlsruhe, Germany.,Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Im Neuenhemier Feld 581, D-69120, Heidelberg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.
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17
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Lynagh T, Kiontke S, Meyhoff-Madsen M, Gless BH, Johannesen J, Kattelmann S, Christiansen A, Dufva M, Laustsen AH, Devkota K, Olsen CA, Kümmel D, Pless SA, Lohse B. Peptide Inhibitors of the α-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction. J Med Chem 2020; 63:13709-13718. [PMID: 33143415 PMCID: PMC7705965 DOI: 10.1021/acs.jmedchem.0c01202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Venomous snakebites cause >100
000 deaths every year, in many cases
via potent depression of human neuromuscular signaling by snake α-neurotoxins.
Emergency therapy still relies on antibody-based antivenom, hampered
by poor access, frequent adverse reactions, and cumbersome production/purification.
Combining high-throughput discovery and subsequent structure–function
characterization, we present simple peptides that bind α-cobratoxin
(α-Cbtx) and prevent its inhibition of nicotinic acetylcholine
receptors (nAChRs) as a lead for the development of alternative antivenoms.
Candidate peptides were identified by phage display and deep sequencing,
and hits were characterized by electrophysiological recordings, leading
to an 8-mer peptide that prevented α-Cbtx inhibition of nAChRs.
We also solved the peptide:α-Cbtx cocrystal structure, revealing
that the peptide, although of unique primary sequence, binds to α-Cbtx
by mimicking structural features of the nAChR binding pocket. This
demonstrates the potential of small peptides to neutralize lethal
snake toxins in vitro, establishing a potential route to simple, synthetic,
low-cost antivenoms.
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Affiliation(s)
- Timothy Lynagh
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.,Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stephan Kiontke
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Maria Meyhoff-Madsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bengt H Gless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jónas Johannesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sabrina Kattelmann
- Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Anders Christiansen
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Martin Dufva
- Fluid Array Systems and Technology, Nano and Bio-physical Systems, Department of Health Technology, Technical University of Denmark, Building 423 Produktionstorvet, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kanchan Devkota
- 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
| | - Daniel Kümmel
- Division of Structural Biology, Department of Biology/Chemistry, University of Osnabrück, Barbarastraße 13, Osnabrück 49076, Germany.,Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Stephan Alexander Pless
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Brian Lohse
- 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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18
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Rajabi N, Nielsen AL, Olsen CA. Dethioacylation by Sirtuins 1-3: Considerations for Drug Design Using Mechanism-Based Sirtuin Inhibition. ACS Med Chem Lett 2020; 11:1886-1892. [PMID: 33062169 DOI: 10.1021/acsmedchemlett.9b00580] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/06/2020] [Indexed: 12/22/2022] Open
Abstract
The sirtuin enzymes are potential drug targets for intervention in a series of diseases. Efforts to inhibit enzymes of this class with thioamide- and thiourea-containing, substrate-mimicking entities have produced a number of high-affinity binders. However, less attention has been dedicated to the investigation of the stability of these inhibitors under various conditions. Here, we provide evidence of an unprecedented degree of cleavage of short-chain ε-N-thioacyllysine modifications meant to target these sirtuins and further provide insights into the serum stability of compounds containing both thioamides and thioureas. Our study questions the utility short-chain thioamide-based inhibitors of sirtuins for drug development and points to monoalkylated thiourea-based chemotypes as being more stable in human serum.
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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
| | - 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
| | - 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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19
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Wellhöfer I, Beck J, Frydenvang K, Bräse S, Olsen CA. Increasing the Functional Group Diversity in Helical β-Peptoids: Achievement of Solvent- and pH-Dependent Folding. J Org Chem 2020; 85:10466-10478. [PMID: 32806085 DOI: 10.1021/acs.joc.0c00780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the synthesis of a series of bis-functionalized β-peptoid oligomers of the hexamer length. This was achieved by synthesizing and incorporating protected amino- or azido-functionalized chiral building blocks into precursor oligomers by a trimer segment coupling strategy. The resulting hexamers were readily elaborated to provide target compounds displaying amino groups, carboxy groups, hydroxy groups, or triazolo-pyridines, which should enable metal ion binding. Analysis of the novel hexamers by circular dichroism (CD) spectroscopy and 1H-13C heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR) spectroscopy revealed robust helical folding propensity in acetonitrile. CD analysis showed a solvent-dependent degree of helical content in the structural ensembles when adding different ratios of protic solvents including an aqueous buffer. These studies were enabled by a substantial increase in solubility compared to previously analyzed β-peptoid oligomers. This also allowed for the investigation of the effect of pH on the folding propensity of the amino- and carboxy-functionalized oligomers, respectively. Interestingly, we could show a reversible effect of sequentially adding acid and base, resulting in a switching between compositions of folded ensembles with varying helical content. We envision that the present discoveries can form the basis for the development of functional peptidomimetic materials responsive to external stimuli.
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Affiliation(s)
- Isabelle Wellhöfer
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Janina Beck
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Stefan Bräse
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen D-76344, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
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20
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Bæk M, Martín‐Gago P, Laursen JS, Madsen JLH, Chakladar S, Olsen CA. Photo Cross-Linking Probes Containing ϵ-N-Thioacyllysine and ϵ-N-Acyl-(δ-aza)lysine Residues. Chemistry 2020; 26:3862-3869. [PMID: 31922630 PMCID: PMC7154546 DOI: 10.1002/chem.201905338] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/07/2020] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications (PTMs) are important in the regulation of protein function, trafficking, localization, and marking for degradation. This work describes the development of peptide activity/affinity-based probes for the discovery of proteins that recognize novel acyl-based PTMs on lysine residues in the proteome. The probes contain surrogates of ϵ-N-acyllysine by introduction of either hydrazide or thioamide functionalities to circumvent hydrolysis of the modification during the experiments. In addition to the modified PTMs, the developed chemotypes were analyzed with respect to the effect of peptide sequence. The photo cross-linking conditions and subsequent functionalization of the covalent adducts were systematically optimized by applying fluorophore labeling and gel electrophoresis (in-gel fluorescence measurements). Finally, selected probes, containing the ϵ-N-glutaryllysine and ϵ-N-myristoyllysine analogues, were successfully applied for the enrichment of native, endogenous proteins from cell lysate, recapitulating the expected interactions of SIRT5 and SIRT2, respectively. Interestingly, the latter mentioned was able to pull down two different splice variants of SIRT2, which has not been achieved with a covalent probe before. Based on this elaborate proof-of-concept study, we expect that the technology will have broad future applications for pairing of novel PTMs with the proteins that target them in the cell.
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Affiliation(s)
- Michael Bæk
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jonas S. Laursen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Julie L. H. Madsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Saswati Chakladar
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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21
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Nielsen AL, Olsen CA. Finding the gas pedal on a slow sirtuin. J Biol Chem 2020; 295:1400-1401. [PMID: 32005646 DOI: 10.1074/jbc.h120.012534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The class III histone deacetylase sirtuin 6 (SIRT6) modulates numerous functions in the cell by deacetylating histone lysine residues. Interestingly, SIRT6's efficiency in in vitro experiments is far greater against substrates carrying long-chain fatty acyl modifications such as myristoylated lysine compared with acetylated counterparts, but the deacetylase activity can be stimulated by fatty acids and small-molecule allosteric modulators. A new study helps to explain this puzzling activation using a novel activator, thorough kinetic investigation, and mutagenesis studies. These data help elucidate the molecular requirements for activation of SIRT6 and provide a foundation for development of activators for therapeutic purposes.
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Affiliation(s)
- Alexander L Nielsen
- Center for Biopharmaceuticals and 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 and 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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23
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Yan D, Franzini A, Pomicter AD, Halverson BJ, Antelope O, Mason CC, Ahmann JM, Senina AV, Vellore NA, Jones CL, Zabriskie MS, Than H, Xiao MJ, van Scoyk A, Patel AB, Clair PM, Heaton WL, Owen SC, Andersen JL, Egbert CM, Reisz JA, D'Alessandro A, Cox JE, Gantz KC, Redwine HM, Iyer SM, Khorashad JS, Rajabi N, Olsen CA, O'Hare T, Deininger MW. SIRT5 IS A DRUGGABLE METABOLIC VULNERABILITY IN ACUTE MYELOID LEUKEMIA. Blood Cancer Discov 2019; 2:266-287. [PMID: 34027418 DOI: 10.1158/2643-3230.bcd-20-0168] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We discovered that the survival and growth of many primary acute myeloid leukemia (AML) samples and cell lines, but not normal CD34+ cells, are dependent on SIRT5, a lysine deacylase implicated in regulating multiple metabolic pathways. Dependence on SIRT5 is genotype-agnostic and extends to RAS- and p53-mutated AML. Results were comparable between SIRT5 knockdown and SIRT5 inhibition using NRD167, a potent and selective SIRT5 inhibitor. Apoptosis induced by SIRT5 disruption is preceded by reductions in oxidative phosphorylation and glutamine utilization, and an increase in mitochondrial superoxide that is attenuated by ectopic superoxide dismutase 2. These data indicate that SIRT5 controls and coordinates several key metabolic pathways in AML and implicate SIRT5 as a vulnerability in AML.
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Affiliation(s)
- Dongqing Yan
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Anca Franzini
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | | | - Orlando Antelope
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Clinton C Mason
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Jonathan M Ahmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Anna V Senina
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nadeem A Vellore
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Courtney L Jones
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Hein Than
- Department of Haematology, Singapore General Hospital, Singapore
| | - Michael J Xiao
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | - Ami B Patel
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Phillip M Clair
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - William L Heaton
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shawn C Owen
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christina M Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Angelo D'Alessandro
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Kevin C Gantz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Hannah M Redwine
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Siddharth M Iyer
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jamshid S Khorashad
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas O'Hare
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Michael W Deininger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
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24
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Peng P, Baldry M, Gless BH, Bojer MS, Espinosa-Gongora C, Baig SJ, Andersen PS, Olsen CA, Ingmer H. Effect of Co-inhabiting Coagulase Negative Staphylococci on S. aureus agr Quorum Sensing, Host Factor Binding, and Biofilm Formation. Front Microbiol 2019; 10:2212. [PMID: 31611856 PMCID: PMC6777374 DOI: 10.3389/fmicb.2019.02212] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/10/2019] [Indexed: 02/04/2023] Open
Abstract
Staphylococcus aureus is a commensal colonizer of both humans and animals, but also an opportunistic pathogen responsible for a multitude of diseases. In recent years, colonization of pigs by methicillin resistant S. aureus has become a problem with increasing numbers of humans being infected by livestock strains. In S. aureus colonization and virulence factor expression is controlled by the agr quorum sensing system, which responds to and is activated by self-generated, autoinducing peptides (AIPs). AIPs are also produced by coagulase negative staphylococci (CoNS) commonly found as commensals in both humans and animals, and interestingly, some of these inhibit S. aureus agr activity. Here, we have addressed if cross-communication occurs between S. aureus and CoNS strains isolated from pig nares, and if so, how properties such as host factor binding and biofilm formation are affected. From 25 pig nasal swabs we obtained 54 staphylococcal CoNS isolates belonging to 8 different species. Of these, none were able to induce S. aureus agr as monitored by reporter gene fusions to agr regulated genes but a number of agr-inhibiting species were identified including Staphylococcus hyicus, Staphylococcus simulans, Staphylococcus arlettae, Staphylococcus lentus, and Staphylococcus chromogenes. After establishing that the inhibitory activity was mediated via AgrC, the receptor of AIPs, we synthesized selective AIPs to explore their effect on adhesion of S. aureus to fibronectin, a host factor involved in S. aureus colonization. Here, we found that the CoNS AIPs did not affect adhesion of S. aureus except for strain 8325-4. When individual CoNS strains were co-cultured together with S. aureus we observed variable degrees of biofilm formation which did not correlate with agr interactions. Our results show that multiple CoNS species can be isolated from pig nares and that the majority of these produce AIPs that inhibit S. aureus agr. Further they show that the consequences of the interactions between CoNS and S. aureus are complex and highly strain dependent.
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Affiliation(s)
- Pai Peng
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mara Baldry
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bengt H Gless
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Martin S Bojer
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carmen Espinosa-Gongora
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sharmin J Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Paal S Andersen
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Christian A Olsen
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Ingmer
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Moreno-Yruela C, Fass DM, Cheng C, Herz J, Olsen CA, Haggarty SJ. Kinetic Tuning of HDAC Inhibitors Affords Potent Inducers of Progranulin Expression. ACS Chem Neurosci 2019; 10:3769-3777. [PMID: 31330099 DOI: 10.1021/acschemneuro.9b00281] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone deacetylases (HDACs) are enzymes involved in the epigenetic control of gene expression. A handful of HDAC inhibitors have been approved for the treatment of cancer, and HDAC inhibition has also been proposed as a novel therapeutic strategy for neurodegenerative disorders. These disorders include progranulin (PGRN)-deficient forms of frontotemporal dementia caused by mutations in the GRN gene that lead to haploinsufficiency. Hydroxamic-acid-based inhibitors of HDACs 1-3, reported to have fast-on/fast-off binding kinetics, induce increased expression of PGRN in human neuronal models, while the benzamide class of slow-binding HDAC inhibitors does not produce this effect. These observations indicate that the kinetics of HDAC inhibitor binding can be tuned for optimal induction of human PGRN expression in neurons. Here, we further expand on these findings using human cortical-like, glutamatergic neurons. We provide evidence that two prototypical, potent hydroxamic acid HDAC inhibitors that induce PGRN (panobinostat and trichostatin A) exhibit an initial fast-binding step followed by a second, slower step, referred to as mechanism B of slow binding, rather than simpler fast-on/fast-off binding kinetics. In addition, we show that trapoxin A, a macrocyclic, epoxyketone-containing class I HDAC inhibitor, exhibits slow binding with high, picomolar potency and also induces PGRN expression in human neurons. Finally, we demonstrate induction of PGRN expression by fast-on/fast-off, highly potent, macrocyclic HDAC inhibitors with ethyl ketone or ethyl ester Zn2+ binding groups. Taken together, these data expand our understanding of HDAC1-3 inhibitor binding kinetics, and further delineate the specific combinations of structural and kinetic features of HDAC inhibitors that are optimal for upregulating PGRN expression in human neurons and thus may have translational relevance in neurodegenerative disease.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Daniel M. Fass
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Chialin Cheng
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Joachim Herz
- Departments of Molecular Genetics, Neuroscience, Neurology and Neurotherapeutics, Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9046, United States
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology & Psychiatry, Massachusetts General Hospital and Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
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26
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Gless BH, Bojer MS, Peng P, Baldry M, Ingmer H, Olsen CA. Identification of autoinducing thiodepsipeptides from staphylococci enabled by native chemical ligation. Nat Chem 2019; 11:463-469. [PMID: 31011175 DOI: 10.1038/s41557-019-0256-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/14/2019] [Indexed: 11/09/2022]
Abstract
Staphylococci secrete autoinducing peptides (AIPs) as signalling molecules to regulate population-wide behaviour. AIPs from non-Staphylococcus aureus staphylococci have received attention as potential antivirulence agents to inhibit quorum sensing and virulence gene expression in the human pathogen Staphylococcus aureus. However, only a limited number of AIP structures from non-S. aureus staphylococci have been identified to date, as the minute amounts secreted in complex media render it difficult. Here, we report a method for the identification of AIPs by exploiting their thiolactone functionality for chemoselective trapping and enrichment of the compounds from the bacterial supernatant. Standard liquid chromatography mass spectrometry analysis, guided by genome sequencing data, then readily provides the AIP identities. Using this approach, we confirm the identity of five known AIPs and identify the AIPs of eleven non-S. aureus species, and we expect that the method should be extendable to AIP-expressing Gram-positive bacteria beyond the Staphylococcus genus.
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Affiliation(s)
- Bengt H Gless
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin S Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pai Peng
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mara Baldry
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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27
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Affiliation(s)
- Isabelle Wellhöfer
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Simona Kotesova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Andreas M. Christiansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jonas S. Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- 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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28
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Martín‐Gago P, Olsen CA. Arylfluorosulfate-Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal. Angew Chem Int Ed Engl 2018; 58:957-966. [PMID: 30024079 PMCID: PMC6518939 DOI: 10.1002/anie.201806037] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Indexed: 01/15/2023]
Abstract
Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.
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Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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29
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Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
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30
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Santner P, Martins JMDS, Kampmeyer C, Hartmann-Petersen R, Laursen JS, Stein A, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants. Biochemistry 2018; 57:5957-5968. [PMID: 30230310 DOI: 10.1021/acs.biochem.8b00722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The influenza M2 proton channel is a major drug target, but unfortunately, the acquisition of resistance mutations greatly reduces the functional life span of a drug in influenza treatment. New M2 inhibitors that inhibit mutant M2 channels otherwise resistant to the early adamantine-based drugs have been reported, but it remains unclear whether and how easy resistance could arise to such inhibitors. We have combined a newly developed proton conduction assay with an established method for selection and screening, both Escherichia coli-based, to enable the study of M2 function and inhibition. Combining this platform with two groups of structurally different M2 inhibitors allowed us to isolate drug resistant M2 channels from a mutant library. Two groups of M2 variants emerged from this analysis. A first group appeared almost unaffected by the inhibitor, M_089 (N13I, I35L, and F47L) and M_272 (G16C and D44H), and the single-substitution variants derived from these (I35L, L43P, D44H, and L46P). Functionally, these resemble the known drug resistant M2 channels V27A, S31N, and swine flu. In addition, a second group of tested M2 variants were all still inhibited by drugs but to a lesser extent than wild type M2. Molecular dynamics simulations aided in distinguishing the two groups where drug binding to the wild type and the less resistant M2 group showed a stable positioning of the ligand in the canonical binding pose, as opposed to the drug resistant group in which the ligand rapidly dissociated from the complex during the simulations.
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Affiliation(s)
- Paul Santner
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - João Miguel da Silva Martins
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Caroline Kampmeyer
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Jonas S Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Amelie Stein
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Christian A Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark.,Center for Biopharmaceuticals, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Isaiah T Arkin
- Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus , Givat-Ram, Jerusalem 91904 , Israel
| | - Jakob R Winther
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
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31
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Santner P, Martins JMDS, Laursen JS, Behrendt L, Riber L, Olsen CA, Arkin IT, Winther JR, Willemoës M, Lindorff-Larsen K. A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel. Biochemistry 2018; 57:5949-5956. [PMID: 30230312 DOI: 10.1021/acs.biochem.8b00721] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The M2 protein is an important target for drugs in the fight against the influenza virus. Because of the emergence of resistance against antivirals directed toward the M2 proton channel, the search for new drugs against resistant M2 variants is of high importance. Robust and sensitive assays for testing potential drug compounds on different M2 variants are valuable tools in this search for new inhibitors. In this work, we describe a fluorescence sensor-based assay, which we termed "pHlux", that measures proton conduction through M2 when synthesized from an expression vector in Escherichia coli. The assay was compared to a previously established bacterial potassium ion transport complementation assay, and the results were compared to simulations obtained from analysis of a computational model of M2 and its interaction with inhibitor molecules. The inhibition of M2 was measured for five different inhibitors, including Rimantadine, Amantadine, and spiro type compounds, and the drug resistance of the M2 mutant variants (swine flu, V27A, and S31N) was confirmed. We demonstrate that the pHlux assay is robust and highly sensitive and shows potential for high-throughput screening.
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Affiliation(s)
- Paul Santner
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - João Miguel da Silva Martins
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Jonas S Laursen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Lars Behrendt
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Leise Riber
- Department of Biology, Section for Microbiology , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Christian A Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark.,Center for Biopharmaceuticals, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Isaiah T Arkin
- Department of Biological Chemistry , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat-Ram , Jerusalem 91904 , Israel
| | - Jakob R Winther
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Section for Biomolecular Sciences, Linderstrøm-Lang Centre for Protein Science , University of Copenhagen , Ole Maaloes Vej 5 , 2200 Copenhagen N, Denmark
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32
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Affiliation(s)
- Bengt H. Gless
- Center for Biopharmaceuticals and 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 and 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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33
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Olesen SV, Rajabi N, Svensson B, Olsen CA, Madsen AS. An NAD +-Dependent Sirtuin Depropionylase and Deacetylase (Sir2La) from the Probiotic Bacterium Lactobacillus acidophilus NCFM. Biochemistry 2018; 57:3903-3915. [PMID: 29863862 DOI: 10.1021/acs.biochem.8b00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sirtuins, a group of NAD+-dependent deacylases, have emerged as the key connection between NAD+ metabolism and aging. This class of enzymes hydrolyzes a range of ε- N-acyllysine PTMs, and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacterium Lactobacillus acidophilus NCFM. Screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, demonstrated that one of the investigated proteins, Sir2La, is a bona fide NAD+-dependent sirtuin, catalyzing hydrolysis of acetyl-, propionyl-, and butyryllysine. Further substantiating the identity of Sir2La as a sirtuin, known sirtuin inhibitors, nicotinamide and suramin, as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. On the basis of steady-state kinetics, Sir2La showed a slight preference for propionyllysine (Kpro) over acetyllysine (Kac). For nonfluorogenic peptide substrates, the preference is driven by a remarkably low KM (280 nM vs 700 nM, for Kpro and Kac, respectively), whereas kcat was similar (21 × 10-3 s-1). Moreover, while NAD+ is a prerequisite for Sir2La-mediated deacylation, Sir2La has a very high KM for NAD+ compared to the expected levels of the dinucleotide in L. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl- and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.
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Affiliation(s)
- Sita V Olesen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine , Technical University of Denmark , DK-2800 Kongens Lyngby , Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, Faculty of Health and Medicinal Sciences , University of Copenhagen , DK-2100 Copenhagen , Denmark.,Department of Drug Design and Pharmacology , University of Copenhagen , DK-2100 Copenhagen , Denmark
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Abstract
Lysine residues across the proteome are modified by posttranslational modifications (PTMs) that significantly enhance the structural and functional diversity of proteins. For lysine, the most abundant PTM is ɛ-N-acetyllysine (Kac), which plays numerous roles in regulation of important cellular functions, such as gene expression (epigenetic effects) and metabolism. A family of enzymes, namely histone deacetylases (HDACs), removes these PTMs. A subset of these enzymes, the sirtuins (SIRTs), represent class III HDAC and, unlike the rest of the family, these hydrolases are NAD+-dependent. Although initially described as deacetylases, alternative deacylase functions for sirtuins have been reported, which expands the potential cellular roles of this class of enzymes. Currently, sirtuins are investigated as therapeutic targets for the treatment of diseases that span from cancers to neurodegenerative disorders. In the present book chapter, we review and discuss the current literature on novel ɛ-N-acyllysine PTMs, targeted by sirtuins, as well as mechanism-based sirtuin inhibitors inspired by their substrates.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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35
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Frontispiece: 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/anie.201784761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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36
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Frontispiz: 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.201784761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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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37
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McDonnell E, Crown SB, Fox DB, Kitir B, Ilkayeva OR, Olsen CA, Grimsrud PA, Hirschey MD. Lipids Reprogram Metabolism to Become a Major Carbon Source for Histone Acetylation. Cell Rep 2017; 17:1463-1472. [PMID: 27806287 DOI: 10.1016/j.celrep.2016.10.012] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/26/2016] [Accepted: 10/04/2016] [Indexed: 01/07/2023] Open
Abstract
Cells integrate nutrient sensing and metabolism to coordinate proper cellular responses to a particular nutrient source. For example, glucose drives a gene expression program characterized by activating genes involved in its metabolism, in part by increasing glucose-derived histone acetylation. Here, we find that lipid-derived acetyl-CoA is a major source of carbon for histone acetylation. Using 13C-carbon tracing combined with acetyl-proteomics, we show that up to 90% of acetylation on certain histone lysines can be derived from fatty acid carbon, even in the presence of excess glucose. By repressing both glucose and glutamine metabolism, fatty acid oxidation reprograms cellular metabolism, leading to increased lipid-derived acetyl-CoA. Gene expression profiling of octanoate-treated hepatocytes shows a pattern of upregulated lipid metabolic genes, demonstrating a specific transcriptional response to lipid. These studies expand the landscape of nutrient sensing and uncover how lipids and metabolism are integrated by epigenetic events that control gene expression.
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Affiliation(s)
- Eoin McDonnell
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, 300 N Duke Street, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Scott B Crown
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, 300 N Duke Street, Durham, NC 27701, USA
| | - Douglas B Fox
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Betül Kitir
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, 300 N Duke Street, Durham, NC 27701, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, 300 N Duke Street, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, 300 N Duke Street, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA.
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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40
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Abstract
The 1,2,3-triazole moiety can be incorporated as a peptide bond bioisostere to provide protease resistance in peptidomimetics. Herein, we report the synthesis of peptidomimetic building blocks containing backbone-fluorinated 1,4-disubstituted 1,2,3-triazole moieties. Synthetic protocols for the preparation of various Xaa-Gly dipeptide surrogates in the form of Xaa-ψ[triazole]-F2Gly building blocks were established, and selected examples were introduced into the endogenous peptide opioid receptor ligand Leu-enkephalin as a model compound.
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Affiliation(s)
- Jens Engel-Andreasen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Isabelle Wellhöfer
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kathrine Wich
- 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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41
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Canovas J, Baldry M, Bojer MS, Andersen PS, Gless BH, Grzeskowiak PK, Stegger M, Damborg P, Olsen CA, Ingmer H. Corrigendum: Cross-Talk between Staphylococcus aureus and Other Staphylococcal Species via the agr Quorum Sensing System. Front Microbiol 2017; 8:1949. [PMID: 29021792 PMCID: PMC5634338 DOI: 10.3389/fmicb.2017.01949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jaime Canovas
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Martin S Bojer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Paal S Andersen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Bengt H Gless
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Piotr K Grzeskowiak
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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42
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Gless BH, Peng P, Pedersen KD, Gotfredsen CH, Ingmer H, Olsen CA. Structure-Activity Relationship Study Based on Autoinducing Peptide (AIP) from Dog Pathogen S. schleiferi. Org Lett 2017; 19:5276-5279. [PMID: 28952740 DOI: 10.1021/acs.orglett.7b02550] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, an effective protocol for solid-phase synthesis of peptide thiolactones by concomitant ring closure and cleavage from the solid support is reported. The strategy was applied for mapping the importance of the structural features in S. schleiferi AIP (5) by performing an alanine scan and truncation of this natural compound. This furnished some of the most potent inhibitors of accessory gene regulator (agr)-I in the human pathogen S. aureus reported to date.
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Affiliation(s)
- Bengt H Gless
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Pai Peng
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen , DK-1870 Frederiksberg C, Denmark
| | - Katja D Pedersen
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, Kgs. Lyngby DK-2800, Denmark
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark , Kemitorvet 207, Kgs. Lyngby DK-2800, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen , DK-1870 Frederiksberg C, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and 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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43
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Anderson KA, Madsen AS, Olsen CA, Hirschey MD. Metabolic control by sirtuins and other enzymes that sense NAD +, NADH, or their ratio. Biochim Biophys Acta Bioenerg 2017; 1858:991-998. [PMID: 28947253 DOI: 10.1016/j.bbabio.2017.09.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 01/12/2023]
Abstract
NAD+ is a dinucleotide cofactor with the potential to accept electrons in a variety of cellular reduction-oxidation (redox) reactions. In its reduced form, NADH is a ubiquitous cellular electron donor. NAD+, NADH, and the NAD+/NADH ratio have long been known to control the activity of several oxidoreductase enzymes. More recently, enzymes outside those participating directly in redox control have been identified that sense these dinucleotides, including the sirtuin family of NAD+-dependent protein deacylases. In this review, we highlight examples of non-redox enzymes that are controlled by NAD+, NADH, or NAD+/NADH. In particular, we focus on the sirtuin family and assess the current evidence that the sirtuin enzymes sense these dinucleotides and discuss the biological conditions under which this might occur; we conclude that sirtuins sense NAD+, but neither NADH nor the ratio. Finally, we identify future studies that might be informative to further interrogate physiological and pathophysiological changes in NAD+ and NADH, as well as enzymes like sirtuins that sense and respond to redox changes in the cell.
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Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, United States; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, United States
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 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, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, United States; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, United States; Department of Medicine, Duke University Medical Center, Durham, NC 27710, United States.
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44
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Kitir B, Maolanon AR, Ohm RG, Colaço AR, Fristrup P, Madsen AS, Olsen CA. Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities. Biochemistry 2017; 56:5134-5146. [DOI: 10.1021/acs.biochem.7b00725] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Betül Kitir
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Alex R. Maolanon
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ragnhild G. Ohm
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ana R. Colaço
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Andreas S. Madsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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45
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Lai JI, Leman LJ, Ku S, Vickers CJ, Olsen CA, Montero A, Ghadiri MR, Gottesfeld JM. Cyclic tetrapeptide HDAC inhibitors as potential therapeutics for spinal muscular atrophy: Screening with iPSC-derived neuronal cells. Bioorg Med Chem Lett 2017. [PMID: 28648462 DOI: 10.1016/j.bmcl.2017.06.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder that is caused by inactivating mutations in the Survival of motor neuron 1 (SMN1) gene, resulting in decreased SMN protein expression. Humans possess a paralog gene, SMN2, which contains a splicing defect in exon 7 leading to diminished expression of full-length, fully functional SMN protein. Increasing SMN2 expression has been a focus of therapeutic development for SMA. Multiple studies have reported the efficacy of histone deacetylase inhibitors (HDACi) in this regard. However, clinical trials involving HDACi have been unsatisfactory, possibly because previous efforts to identify HDACi to treat SMA have employed non-neuronal cells as the screening platform. To address this issue, we generated an SMA-patient specific, induced pluripotent stem cell (iPSC) derived neuronal cell line that contains homogenous Tuj1+neurons. We screened a small library of cyclic tetrapeptide HDACi using this SMA neuronal platform and discovered compounds that elevate SMN2 expression by an impressive twofold or higher. These candidates are also capable of forming gems intranuclearly in SMA neurons, demonstrating biological activity. Our study identifies new potential HDACi therapeutics for SMA screened using a disease-relevant SMA neuronal cellular model.
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Affiliation(s)
- Jiun-I Lai
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; National Yang-Ming University, Taipei, Taiwan; National Yang-Ming University Hospital, Ilan, Taiwan
| | - Luke J Leman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Sherman Ku
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Chris J Vickers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christian A Olsen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA; Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ana Montero
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - M Reza Ghadiri
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joel M Gottesfeld
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.
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Canovas J, Baldry M, Bojer MS, Andersen PS, Grzeskowiak PK, Stegger M, Damborg P, Olsen CA, Ingmer H. Corrigendum: Cross-Talk between Staphylococcus aureus and Other Staphylococcal Species via the agr Quorum Sensing System. Front Microbiol 2017; 8:1075. [PMID: 28607550 PMCID: PMC5463500 DOI: 10.3389/fmicb.2017.01075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/29/2017] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article on p. 1733 in vol. 7, PMID: 27877157.].
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Affiliation(s)
- Jaime Canovas
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Martin S Bojer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Paal S Andersen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark.,Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Piotr K Grzeskowiak
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Peter Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark
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Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD. SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion. Cell Metab 2017; 25:838-855.e15. [PMID: 28380376 PMCID: PMC5444661 DOI: 10.1016/j.cmet.2017.03.003] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 09/26/2016] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
Abstract
Sirtuins are NAD+-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine. The metabolites leading to these post-translational modifications are intermediates in leucine oxidation, and we show a primary role for SIRT4 in controlling this pathway in mice. Furthermore, we find that dysregulated leucine metabolism in SIRT4KO mice leads to elevated basal and stimulated insulin secretion, which progressively develops into glucose intolerance and insulin resistance. These findings identify a robust enzymatic activity for SIRT4, uncover a mechanism controlling branched-chain amino acid flux, and position SIRT4 as a crucial player maintaining insulin secretion and glucose homeostasis during aging.
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Affiliation(s)
- Kristin A Anderson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Kelsey Fisher-Wellman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Darren Stuart
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Brett S Peterson
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Jonathan D Douros
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Gregory R Wagner
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - Andreas S Madsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Michelle F Green
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - R Michael Sivley
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Olga R Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Robert D Stevens
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John A Capra
- Department of Biological Sciences, Department of Biomedical Informatics, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jonathan E Campbell
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Deborah M Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul A Grimsrud
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC 27710, USA.
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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Canovas J, Baldry M, Bojer MS, Andersen PS, Grzeskowiak PK, Stegger M, Damborg P, Olsen CA, Ingmer H. Cross-Talk between Staphylococcus aureus and Other Staphylococcal Species via the agr Quorum Sensing System. Front Microbiol 2016; 7:1733. [PMID: 27877157 PMCID: PMC5099252 DOI: 10.3389/fmicb.2016.01733] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
Staphylococci are associated with both humans and animals. While most are non-pathogenic colonizers, Staphylococcus aureus is an opportunistic pathogen capable of causing severe infections. S. aureus virulence is controlled by the agr quorum sensing system responding to secreted auto-inducing peptides (AIPs) sensed by AgrC, a two component histidine kinase. agr loci are found also in other staphylococcal species and for Staphylococcus epidermidis, the encoded AIP represses expression of agr regulated virulence genes in S. aureus. In this study we aimed to better understand the interaction between staphylococci and S. aureus, and show that this interaction may eventually lead to the identification of new anti-virulence candidates to target S. aureus infections. Here we show that culture supernatants of 37 out of 52 staphylococcal isolates representing 17 different species inhibit S. aureus agr. The dog pathogen, Staphylococcus schleiferi, expressed the most potent inhibitory activity and was active against all four agr classes found in S. aureus. By employing a S. aureus strain encoding a constitutively active AIP receptor we show that the activity is mediated via agr. Subsequent cloning and heterologous expression of the S. schleiferi AIP in S. aureus demonstrated that this molecule was likely responsible for the inhibitory activity, and further proof was provided when pure synthetic S. schleiferi AIP was able to completely abolish agr induction of an S. aureus reporter strain. To assess impact on S. aureus virulence, we co-inoculated S. aureus and S. schleiferi in vivo in the Galleria mellonella wax moth larva, and found that expression of key S. aureus virulence factors was abrogated. Our data show that the S. aureus agr locus is highly responsive to other staphylococcal species suggesting that agr is an inter-species communication system. Based on these results we speculate that interactions between S. aureus and other colonizing staphylococci will significantly influence the ability of S. aureus to cause infection, and we propose that other staphylococci are potential sources of compounds that can be applied as anti-virulence therapy for combating S. aureus infections.
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Affiliation(s)
- Jaime Canovas
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Martin S Bojer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Paal S Andersen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark; Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Piotr K Grzeskowiak
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut Copenhagen, Denmark
| | - Peter Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
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