1
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Fiorentino F, Fabbrizi E, Mai A, Rotili D. Activation and inhibition of sirtuins: From bench to bedside. Med Res Rev 2024. [PMID: 39215785 DOI: 10.1002/med.22076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/27/2024] [Accepted: 08/04/2024] [Indexed: 09/04/2024]
Abstract
The sirtuin family comprises seven NAD+-dependent enzymes which catalyze protein lysine deacylation and mono ADP-ribosylation. Sirtuins act as central regulators of genomic stability and gene expression and control key processes, including energetic metabolism, cell cycle, differentiation, apoptosis, and aging. As a result, all sirtuins play critical roles in cellular homeostasis and organism wellness, and their dysregulation has been linked to metabolic, cardiovascular, and neurological diseases. Furthermore, sirtuins have shown dichotomous roles in cancer, acting as context-dependent tumor suppressors or promoters. Given their central role in different cellular processes, sirtuins have attracted increasing research interest aimed at developing both activators and inhibitors. Indeed, sirtuin modulation may have therapeutic effects in many age-related diseases, including diabetes, cardiovascular and neurodegenerative disorders, and cancer. Moreover, isoform selective modulators may increase our knowledge of sirtuin biology and aid to develop better therapies. Through this review, we provide critical insights into sirtuin pharmacology and illustrate their enzymatic activities and biological functions. Furthermore, we outline the most relevant sirtuin modulators in terms of their modes of action, structure-activity relationships, pharmacological effects, and clinical applications.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Emanuele Fabbrizi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
- Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
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2
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Colcerasa A, Friedrich F, Melesina J, Moser P, Vogelmann A, Tzortzoglou P, Neuwirt E, Sum M, Robaa D, Zhang L, Ramos-Morales E, Romier C, Einsle O, Metzger E, Schüle R, Groß O, Sippl W, Jung M. Structure-Activity Studies of 1,2,4-Oxadiazoles for the Inhibition of the NAD +-Dependent Lysine Deacylase Sirtuin 2. J Med Chem 2024; 67:10076-10095. [PMID: 38847803 DOI: 10.1021/acs.jmedchem.4c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The NAD+-dependent lysine deacylase sirtuin 2 (Sirt2) is involved in multiple pathological conditions such as cancer. Targeting Sirt2 has thus received an increased interest for therapeutic purposes. Furthermore, the orthologue from Schistosoma mansoni (SmSirt2) has been considered for the potential treatment of the neglected tropical disease schistosomiasis. We previously identified a 1,2,4-oxadiazole-based scaffold from the screening of the "Kinetobox" library as a dual inhibitor of human Sirt2 (hSirt2) and SmSirt2. Herein, we describe the structure-activity studies on 1,2,4-oxadiazole-based analogues, which are potent inhibitors of human Sirt2 deacetylation. As proposed by docking studies, a substrate-competitive and cofactor-noncompetitive binding mode of inhibition could be determined in vitro via binding assays and kinetic analysis and further confirmed by a crystal structure of an oxadiazole inhibitor in complex with hSirt2. Optimized analogues reduced cell viability and inhibited prostate cancer cell migration, in correlation with Sirt2 deacetylase inhibition both in vitro and in cells.
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Affiliation(s)
- Arianna Colcerasa
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
| | - Florian Friedrich
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
| | - Jelena Melesina
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, Halle/Saale 06120, Germany
| | - Patrick Moser
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
| | - Anja Vogelmann
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
- CIBSS─Centre for Integrative Biological Signalling Studies, Freiburg 79104, Germany
| | - Pavlos Tzortzoglou
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
| | - Emilia Neuwirt
- Institute of Neuropathology, University of Freiburg Medical Center, Breisacher Straße 113, Freiburg 79106, Germany
| | - Manuela Sum
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center, Breisacher Straße 66, Freiburg 79106, Germany
| | - Dina Robaa
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, Halle/Saale 06120, Germany
| | - Lin Zhang
- Institute of Biochemistry, University of Freiburg, Albertstraße 21, Freiburg 79104, Germany
| | - Elizabeth Ramos-Morales
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm UMR-S 1258, 1 Rue Laurent Fries, Illkirch F-67400, France
| | - Christophe Romier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm UMR-S 1258, 1 Rue Laurent Fries, Illkirch F-67400, France
| | - Oliver Einsle
- Institute of Biochemistry, University of Freiburg, Albertstraße 21, Freiburg 79104, Germany
| | - Eric Metzger
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center, Breisacher Straße 66, Freiburg 79106, Germany
| | - Roland Schüle
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center, Breisacher Straße 66, Freiburg 79106, Germany
- CIBSS─Centre for Integrative Biological Signalling Studies, Freiburg 79104, Germany
| | - Olaf Groß
- Institute of Neuropathology, University of Freiburg Medical Center, Breisacher Straße 113, Freiburg 79106, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, Halle/Saale 06120, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
- CIBSS─Centre for Integrative Biological Signalling Studies, Freiburg 79104, Germany
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3
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Scarano N, Brullo C, Musumeci F, Millo E, Bruzzone S, Schenone S, Cichero E. Recent Advances in the Discovery of SIRT1/2 Inhibitors via Computational Methods: A Perspective. Pharmaceuticals (Basel) 2024; 17:601. [PMID: 38794171 PMCID: PMC11123952 DOI: 10.3390/ph17050601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Sirtuins (SIRTs) are classified as class III histone deacetylases (HDACs), a family of enzymes that catalyze the removal of acetyl groups from the ε-N-acetyl lysine residues of histone proteins, thus counteracting the activity performed by histone acetyltransferares (HATs). Based on their involvement in different biological pathways, ranging from transcription to metabolism and genome stability, SIRT dysregulation was investigated in many diseases, such as cancer, neurodegenerative disorders, diabetes, and cardiovascular and autoimmune diseases. The elucidation of a consistent number of SIRT-ligand complexes helped to steer the identification of novel and more selective modulators. Due to the high diversity and quantity of the structural data thus far available, we reviewed some of the different ligands and structure-based methods that have recently been used to identify new promising SIRT1/2 modulators. The present review is structured into two sections: the first includes a comprehensive perspective of the successful computational approaches related to the discovery of SIRT1/2 inhibitors (SIRTIs); the second section deals with the most interesting SIRTIs that have recently appeared in the literature (from 2017). The data reported here are collected from different databases (SciFinder, Web of Science, Scopus, Google Scholar, and PubMed) using "SIRT", "sirtuin", and "sirtuin inhibitors" as keywords.
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Affiliation(s)
- Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Francesca Musumeci
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Silvia Schenone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
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4
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Chen M, Tan J, Jin Z, Jiang T, Wu J, Yu X. Research progress on Sirtuins (SIRTs) family modulators. Biomed Pharmacother 2024; 174:116481. [PMID: 38522239 DOI: 10.1016/j.biopha.2024.116481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Sirtuins (SIRTs) represent a class of nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylases that exert a crucial role in cellular signal transduction and various biological processes. The mammalian sirtuins family encompasses SIRT1 to SIRT7, exhibiting therapeutic potential in counteracting cellular aging, modulating metabolism, responding to oxidative stress, inhibiting tumors, and improving cellular microenvironment. These enzymes are intricately linked to the occurrence and treatment of diverse pathological conditions, including cancer, autoimmune diseases, and cardiovascular disorders. Given the significance of histone modification in gene expression and chromatin structure, maintaining the equilibrium of the sirtuins family is imperative for disease prevention and health restoration. Mounting evidence suggests that modulators of SIRTs play a crucial role in treating various diseases and maintaining physiological balance. This review delves into the molecular structure and regulatory functions of the sirtuins family, reviews the classification and historical evolution of SIRTs modulators, offers a systematic overview of existing SIRTs modulation strategies, and elucidates the regulatory mechanisms of SIRTs modulators (agonists and inhibitors) and their clinical applications. The article concludes by summarizing the challenges encountered in SIRTs modulator research and offering insights into future research directions.
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Affiliation(s)
- Mingkai Chen
- Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China; School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Junfei Tan
- School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zihan Jin
- Changzhou Second People's Hospital Affiliated to Nanjing Medical University, Changzhou City, China
| | - Tingting Jiang
- Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
| | - Jiabiao Wu
- Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China
| | - Xiaolong Yu
- Wujin Hospital Affiliated with Jiangsu University, Changzhou, Jiangsu, China; The Wujin Clinical College of Xuzhou Medical University, Changzhou, Jiangsu, China.
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5
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Suzuki N, Konuma T, Ikegami T, Akashi S. Biophysical insights into the dimer formation of human Sirtuin 2. Protein Sci 2024; 33:e4994. [PMID: 38647411 PMCID: PMC11034489 DOI: 10.1002/pro.4994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/16/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild-type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52-357) forms a homodimer in a concentration-dependent manner with a dimer-monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non-dimerizing mutants exhibited deacetylation activity for the N-terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292-306, which lacks a SIRT2-specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X-ray structure of the mutant Δ292-306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.
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Affiliation(s)
- Noa Suzuki
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City UniversityYokohamaKanagawaJapan
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6
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Bursch KL, Goetz CJ, Smith BC. Current Trends in Sirtuin Activator and Inhibitor Development. Molecules 2024; 29:1185. [PMID: 38474697 DOI: 10.3390/molecules29051185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Sirtuins are NAD+-dependent protein deacylases and key metabolic regulators, coupling the cellular energy state with selective lysine deacylation to regulate many downstream cellular processes. Humans encode seven sirtuin isoforms (Sirt1-7) with diverse subcellular localization and deacylase targets. Sirtuins are considered protective anti-aging proteins since increased sirtuin activity is canonically associated with lifespan extension and decreased activity with developing aging-related diseases. However, sirtuins can also assume detrimental cellular roles where increased activity contributes to pathophysiology. Modulation of sirtuin activity by activators and inhibitors thus holds substantial potential for defining the cellular roles of sirtuins in health and disease and developing therapeutics. Instead of being comprehensive, this review discusses the well-characterized sirtuin activators and inhibitors available to date, particularly those with demonstrated selectivity, potency, and cellular activity. This review also provides recommendations regarding the best-in-class sirtuin activators and inhibitors for practical research as sirtuin modulator discovery and refinement evolve.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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7
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Kaya SG, Eren G. Selective inhibition of SIRT2: A disputable therapeutic approach in cancer therapy. Bioorg Chem 2024; 143:107038. [PMID: 38113655 DOI: 10.1016/j.bioorg.2023.107038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/23/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Sirtuin 2 (SIRT2) is involved in a wide range of processes, from transcription to metabolism to genome stability. Dysregulation of SIRT2 has been associated with the pathogenesis and progression of different diseases, such as cancer and neurodegenerative disorders. In this context, targeting SIRT2 activity by small molecule inhibitors is a promising therapeutic strategy for treating related conditions, particularly cancer. This review summarizes the regulatory roles and molecular mechanisms of SIRT2 in cancer and the attempts to evaluate potential antitumor activities of SIRT2-selective inhibitors by in vitro and in vivo testing, which are expected to deepen our understanding of the role of SIRT2 in tumorigenesis and progression and may offer important clues or inspiration ideas for developing SIRT2 inhibitors with excellent affinity and selectivity.
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Affiliation(s)
- Selen Gozde Kaya
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
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8
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Sinatra L, Vogelmann A, Friedrich F, Tararina MA, Neuwirt E, Colcerasa A, König P, Toy L, Yesiloglu TZ, Hilscher S, Gaitzsch L, Papenkordt N, Zhai S, Zhang L, Romier C, Einsle O, Sippl W, Schutkowski M, Gross O, Bendas G, Christianson DW, Hansen FK, Jung M, Schiedel M. Development of First-in-Class Dual Sirt2/HDAC6 Inhibitors as Molecular Tools for Dual Inhibition of Tubulin Deacetylation. J Med Chem 2023; 66:14787-14814. [PMID: 37902787 PMCID: PMC10641818 DOI: 10.1021/acs.jmedchem.3c01385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023]
Abstract
Dysregulation of both tubulin deacetylases sirtuin 2 (Sirt2) and the histone deacetylase 6 (HDAC6) has been associated with the pathogenesis of cancer and neurodegeneration, thus making these two enzymes promising targets for pharmaceutical intervention. Herein, we report the design, synthesis, and biological characterization of the first-in-class dual Sirt2/HDAC6 inhibitors as molecular tools for dual inhibition of tubulin deacetylation. Using biochemical in vitro assays and cell-based methods for target engagement, we identified Mz325 (33) as a potent and selective inhibitor of both target enzymes. Inhibition of both targets was further confirmed by X-ray crystal structures of Sirt2 and HDAC6 in complex with building blocks of 33. In ovarian cancer cells, 33 evoked enhanced effects on cell viability compared to single or combination treatment with the unconjugated Sirt2 and HDAC6 inhibitors. Thus, our dual Sirt2/HDAC6 inhibitors are important new tools to study the consequences and the therapeutic potential of dual inhibition of tubulin deacetylation.
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Affiliation(s)
- Laura Sinatra
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Anja Vogelmann
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Florian Friedrich
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Margarita A. Tararina
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Emilia Neuwirt
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
| | - Arianna Colcerasa
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Philipp König
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Talha Z. Yesiloglu
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Sebastian Hilscher
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Lena Gaitzsch
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Niklas Papenkordt
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Shiyang Zhai
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lin Zhang
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Christophe Romier
- Institut
de Génétique et de Biologie Moléculaire et Cellulaire
(IGBMC), Université de Strasbourg,
CNRS UMR 7104, Inserm UMR-S 1258, 1 rue Laurent Fries, F-67400 Illkirch, France
| | - Oliver Einsle
- Institute
of Biochemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Wolfgang Sippl
- Department
of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Wolfgang-Langenbeck-Straße 2-4, 06120 Halle (Saale), Germany
| | - Mike Schutkowski
- Department
of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry
and Biotechnology, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Olaf Gross
- Institute
of Neuropathology, Medical Center−University of Freiburg, Faculty
of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
- CIBSS−Centre
for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Center
for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Breisacherstraße 64, 79106 Freiburg, Germany
| | - Gerd Bendas
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Finn K. Hansen
- Institute
for Drug Discovery, Medical Faculty, Leipzig
University, Brüderstraße 34, 04103 Leipzig, Germany
- Department
of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical
Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, University of
Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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9
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Scarano N, Abbotto E, Musumeci F, Salis A, Brullo C, Fossa P, Schenone S, Bruzzone S, Cichero E. Virtual Screening Combined with Enzymatic Assays to Guide the Discovery of Novel SIRT2 Inhibitors. Int J Mol Sci 2023; 24:ijms24119363. [PMID: 37298312 DOI: 10.3390/ijms24119363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Sirtuin isoform 2 (SIRT2) is one of the seven sirtuin isoforms present in humans, being classified as class III histone deacetylases (HDACs). Based on the high sequence similarity among SIRTs, the identification of isoform selective modulators represents a challenging task, especially for the high conservation observed in the catalytic site. Efforts in rationalizing selectivity based on key residues belonging to the SIRT2 enzyme were accompanied in 2015 by the publication of the first X-ray crystallographic structure of the potent and selective SIRT2 inhibitor SirReal2. The subsequent studies led to different experimental data regarding this protein in complex with further different chemo-types as SIRT2 inhibitors. Herein, we reported preliminary Structure-Based Virtual Screening (SBVS) studies using a commercially available library of compounds to identify novel scaffolds for the design of new SIRT2 inhibitors. Biochemical assays involving five selected compounds allowed us to highlight the most effective chemical features supporting the observed SIRT2 inhibitory ability. This information guided the following in silico evaluation and in vitro testing of further compounds from in-house libraries of pyrazolo-pyrimidine derivatives towards novel SIRT2 inhibitors (1-5). The final results indicated the effectiveness of this scaffold for the design of promising and selective SIRT2 inhibitors, featuring the highest inhibition among the tested compounds, and validating the applied strategy.
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Affiliation(s)
- Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Elena Abbotto
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Francesca Musumeci
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Annalisa Salis
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Silvia Schenone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
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10
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Pokhodylo N, Finiuk N, Klyuchivska O, Stoika R, Matiychuk V, Obushak M. Bioisosteric replacement of 1H-1,2,3-triazole with 1H-tetrazole ring enhances anti-leukemic activity of (5-benzylthiazol-2-yl)benzamides. Eur J Med Chem 2023; 250:115126. [PMID: 36809707 DOI: 10.1016/j.ejmech.2023.115126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/26/2023]
Abstract
Previously, we discovered that N-(5-benzyl-1,3-thiazol-2-yl)-4-(5-methyl-1H-1,2,3-triazol-1-yl)benzamide possessed a remarkable cytotoxic effect on 28 cancer cell lines with IC50 < 50 μM, including 9 cancer cell lines, where IC50 was in the range of 2.02-4.70 μM. In the present study, we designed a novel N-(5-benzylthiazol-2-yl)amide compound 3d that was synthesized using the original bioisosteric replacement of 1H-1,2,3-triazole ring by the 1H-tetrazole ring. A significantly enhanced anticancer activity in vitro with an excellent anti-leukemic potency towards chronic myeloid leukemia cells of the K-562 line was demonstrated. Two compounds - 3d and 3l - were highly cytotoxic at nanomolar concentrations towards various tumor cells of the following lines: K-562, NCI-H460, HCT-15, KM12, SW-620, LOX IMVI, M14, UACC-62, CAKI-1, and T47D. As a highlight, the compound N-(5-(4-fluorobenzyl)thiazol-2-yl)-4-(1H-tetrazol-1-yl)benzamide 3d inhibited the growth of leukemia K-562 cells and melanoma UACC-62 cells with IС50 of 56.4 and 56.9 nM (SRB test), respectively. The viability of leukemia K-562 and pseudo-normal HaCaT, NIH-3T3, and J774.2 cells was measured by the MTT assay. Together with SAR analysis, it allowed the selection of a lead compound 3d, which demonstrated the highest selectivity (SI = 101.0) towards treated leukemic cells. The compound 3d caused DNA damage (single-strand breaks detected by the alkaline comet assay) in the leukemic K-562 cells. The morphological study of the K-562 cells treated with compound 3d revealed changes consistent with apoptosis. Thus, the bioisosteric replacement in (5-benzylthiazol-2-yl)amide scaffold proved to be a perspective approach in the design of novel heterocyclic compounds with enhanced anticancer potential.
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Affiliation(s)
- Nazariy Pokhodylo
- Ivan Franko National University of Lviv, Kyryla and Mefodiya Str., 6, 79005, Lviv, Ukraine.
| | - Nataliya Finiuk
- Ivan Franko National University of Lviv, Kyryla and Mefodiya Str., 6, 79005, Lviv, Ukraine; Institute of Cell Biology of National Academy of Sciences of Ukraine, Drahomanov Str., 14/16, 79005, Lviv, Ukraine
| | - Olha Klyuchivska
- Institute of Cell Biology of National Academy of Sciences of Ukraine, Drahomanov Str., 14/16, 79005, Lviv, Ukraine
| | - Rostyslav Stoika
- Ivan Franko National University of Lviv, Kyryla and Mefodiya Str., 6, 79005, Lviv, Ukraine; Institute of Cell Biology of National Academy of Sciences of Ukraine, Drahomanov Str., 14/16, 79005, Lviv, Ukraine
| | - Vasyl Matiychuk
- Ivan Franko National University of Lviv, Kyryla and Mefodiya Str., 6, 79005, Lviv, Ukraine
| | - Mykola Obushak
- Ivan Franko National University of Lviv, Kyryla and Mefodiya Str., 6, 79005, Lviv, Ukraine
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11
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He J, Qiu N, Zhou X, Meng M, Liu Z, Li J, Du S, Sun Z, Wang H. Resveratrol analog, triacetylresveratrol, a potential immunomodulator of lung adenocarcinoma immunotherapy combination therapies. Front Oncol 2023; 12:1007653. [PMID: 36844923 PMCID: PMC9947150 DOI: 10.3389/fonc.2022.1007653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/01/2022] [Indexed: 02/11/2023] Open
Abstract
Introduction Resveratrol, an activator for longevity regulatory genes-sirtuin family (SIRTs) and Sirtuin 2 (SIRT2) is an important factor of SIRTs which demonstrated biological function in cancers, but the underlying mechanism is unrevealed. Methods We investigated the mRNA and protein levels of SIRT2 in a variety of cancers and the potential role for clinical prognosis, as well as analysed the association between the gene and immune infiltration in various cancers. And an analysis of two types of lung cancer was conducted to construct a systematic prognostic landscape. Finally, putative binding site of the triacetylresveratrol bound to SIRT2 was built from homology modeling. Results and discussion We concluded that higher mRNA and protein levels of SIRT2 affected prognosis in various types of cancers, especially in LUAD cohorts. In addition, SIRT2 is linked with a better overall survival (OS) in LUAD patients. Further research suggested a possible explanation for this phenotype might be that SIRT2 mRNA levels are positively correlated with infiltrating status of multiple immunocytes in LU-AD but not LUSC, i.e. SIRT2 expression may contribute to the recruitment of CD8+T cell, CD4+ T cell, T cell CD4+ memory resting, Tregs, T cell NK and positively correlated to the expression of PD-1, also excluding neutrophil, T cell CD8+ naïve and B cell plasma cells in LUAD. We found that triacetyl-resveratrol demonstrated the most potent agonist efficiency to SIRT2 and the EC 50 as low as 142.79 nM. As a result, SIRT2 appears to be a promising novel biomarker for prognosis prediction in patients with LUAD and triacetylresveratrol might be a potential immunomodulator of LUAD to anti-PD-1 based immunotherapy combination therapies.
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Affiliation(s)
- Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Nianxiang Qiu
- Department of Interventional Radiology, The Tumor Hospital of Jilin Province, Changchun, China
- Engineering Laboratory of Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Xianchao Zhou
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mei Meng
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zixue Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingquan Li
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyu Du
- Engineering Laboratory of Nuclear Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, Zhejiang, China
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, China
| | - Zhiqiang Sun
- Department of Interventional Radiology, The Tumor Hospital of Jilin Province, Changchun, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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In silico drug discovery of SIRT2 inhibitors from natural source as anticancer agents. Sci Rep 2023; 13:2146. [PMID: 36750593 PMCID: PMC9905574 DOI: 10.1038/s41598-023-28226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Sirtuin 2 (SIRT2) is a member of the sirtuin protein family, which includes lysine deacylases that are NAD+-dependent and organize several biological processes. Different forms of cancer have been associated with dysregulation of SIRT2 activity. Hence, identifying potent inhibitors for SIRT2 has piqued considerable attention in the drug discovery community. In the current study, the Natural Products Atlas (NPAtlas) database was mined to hunt potential SIRT2 inhibitors utilizing in silico techniques. Initially, the performance of the employed docking protocol to anticipate ligand-SIRT2 binding mode was assessed according to the accessible experimental data. Based on the predicted docking scores, the most promising NPAtlas molecules were selected and submitted to molecular dynamics (MD) simulations, followed by binding energy computations. Based on the MM-GBSA binding energy estimations over a 200 ns MD course, three NPAtlas compounds, namely NPA009578, NPA006805, and NPA001884, were identified with better ΔGbinding towards SIRT2 protein than the native ligand (SirReal2) with values of - 59.9, - 57.4, - 53.5, and - 49.7 kcal/mol, respectively. On the basis of structural and energetic assessments, the identified NPAtlas compounds were confirmed to be steady over a 200 ns MD course. The drug-likeness and pharmacokinetic characteristics of the identified NPAtlas molecules were anticipated, and robust bioavailability was predicted. Conclusively, the current results propose potent inhibitors for SIRT2 deserving more in vitro/in vivo investigation.
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13
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Abstract
Sirtuins are NAD+-dependent protein lysine deacylase and mono-ADP ribosylases present in both prokaryotes and eukaryotes. The sirtuin family comprises seven isoforms in mammals, each possessing different subcellular localization and biological functions. Sirtuins have received increasing attention in the past two decades given their pivotal functions in a variety of biological contexts, including cytodifferentiation, transcriptional regulation, cell cycle progression, apoptosis, inflammation, metabolism, neurological and cardiovascular physiology and cancer. Consequently, modulation of sirtuin activity has been regarded as a promising therapeutic option for many pathologies. In this review, we provide an up-to-date overview of sirtuin biology and pharmacology. We examine the main features of the most relevant inhibitors and activators, analyzing their structure-activity relationships, applications in biology, and therapeutic potential.
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14
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Vaca HR, Celentano AM, Toscanini MA, Hauser AT, Macchiaroli N, Cuestas ML, Nusblat AD, Sippl W, Elissondo MC, Jung M, Camicia F, Rosenzvit MC. Identification and characterization of sirtuin enzymes in cestodes and evaluation of sirtuin inhibitors as new cestocidal molecules. Int J Parasitol 2022; 52:317-329. [PMID: 35150663 DOI: 10.1016/j.ijpara.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/05/2022]
Abstract
Anti-parasitic treatment of neglected tropical diseases (NTDs) caused by cestodes such as echinococcosis and cysticercosis relies on a small number of approved anthelmintic drugs. Furthermore, the treatment is usually prolonged and often partially effective and not well tolerated by some patients. Therefore, the identification of novel drug targets and their associated compounds is critical. In this study, we identified and characterized sirtuin (SIRT) enzymes in cestodes and evaluated the cestocidal potential of SIRT inhibitors. SIRTs are a highly conserved family of nicotinamide-adenine dinucleotide (NAD+)-lysine deacylases involved in multiple cellular functions. Here, we described the full repertoire of SIRT-encoding genes in several cestode species. We identified six SIRT-encoding genes that were classified into SIRTs Class I (SIRT1, SIRT2, and SIRT3), Class III (SIRT5), and Class IV (SIRT6 and SIRT7). In Echinococcus spp., SIRT genes showed transcriptional expression throughout several developmental stages, SIRT2 being the most expressed. To evaluate the potential of SIRT inhibitors as new cestocidal molecules, we determined the in vitro effect of several Class I SIRT inhibitors by motility assay. Of those, the selective SIRT2 inhibitor Mz25 showed a strong cestocidal activity in Mesocestoides vogae (syn. Mesocestoides corti) tetrathyridia at various concentrations. The Mz25 cestocidal activity was time- and dose-dependent with a half-maximal inhibitory concentration (IC50) value significantly lower than that of albendazole. Additionally, Mz25 induced extensive damage in the general morphology with marked alterations in the tegument and ultrastructural features. By homology modeling, we found that cestode SIRT2s showed a high conservation of the canonical SIRT structure as well as in the residues related to Mz25 binding. Interestingly, some non-conservative mutations were found on the selectivity pocket (an Mz25-induced structural rearrangement on the active site), which represent a promising lead for developing selective cestode SIRT2 inhibitors derived from Mz25. Nevertheless, the Mz25 molecular target in M. vogae is unknown and remains to be determined. This report provides the basis for further studies of SIRTs to understand their roles in cestode biology and to develop selective SIRT inhibitors to treat these parasitic NTDs.
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Affiliation(s)
- Hugo Rolando Vaca
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana María Celentano
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Agustina Toscanini
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Natalia Macchiaroli
- Laboratorio de Genómica y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - María Luján Cuestas
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro David Nusblat
- Universidad de Buenos Aires (UBA), CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Ciudad Autónoma de Buenos Aires, Argentina
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle(Saale), Germany
| | - María Celina Elissondo
- Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales - UNMdP, Centro Científico Tecnológico Mar del Plata - CONICET, Centro de Asociación Simple CIC PBA, Mar del Plata, Argentina; Laboratorio de Zoonosis Parasitarias, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Federico Camicia
- Laboratorio de Toxinopatología, Centro de Patología Experimental y Aplicada, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires (UBA), CONICET, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Ciudad Autónoma de Buenos Aires, Argentina.
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15
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Vogelmann A, Schiedel M, Wössner N, Merz A, Herp D, Hammelmann S, Colcerasa A, Komaniecki G, Hong JY, Sum M, Metzger E, Neuwirt E, Zhang L, Einsle O, Groß O, Schüle R, Lin H, Sippl W, Jung M. Development of a NanoBRET assay to validate dual inhibitors of Sirt2-mediated lysine deacetylation and defatty-acylation that block prostate cancer cell migration. RSC Chem Biol 2022; 3:468-485. [PMID: 35441145 PMCID: PMC8985159 DOI: 10.1039/d1cb00244a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Sirtuin2 (Sirt2) with its NAD+-dependent deacetylase and defatty-acylase activities plays a central role in the regulation of specific cellular functions. Dysregulation of Sirt2 activity has been associated with the pathogenesis of many diseases, thus making Sirt2 a promising target for pharmaceutical intervention. Herein, we present new high affinity Sirt2 selective Sirtuin-Rearranging Ligands (SirReals) that inhibit both Sirt2-dependent deacetylation and defatty-acylation in vitro and in cells. We show that simultaneous inhibition of both Sirt2 activities results in strongly reduced levels of the oncoprotein c-Myc and an inhibition of cancer cell migration. Furthermore, we describe the development of a NanoBRET-based assay for Sirt2, thereby providing a method to study cellular target engagement for Sirt2 in a straightforward and accurately quantifiable manner. Applying this assay, we could confirm cellular Sirt2 binding of our new Sirt2 inhibitors and correlate their anticancer effects with their cellular target engagement. Sirt2 inhibitors that show simultaneous inhibition of Sirt2 deacetylase and defatty-acylase activity block prostate cancer cell migration and their target engagement is shown by a newly developed NanoBRET assay.![]()
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Affiliation(s)
- A Vogelmann
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - M Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg Nikolaus-Fiebiger-Straße 10 91058 Erlangen Germany
| | - N Wössner
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - A Merz
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - D Herp
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - S Hammelmann
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - A Colcerasa
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
| | - G Komaniecki
- Department of Chemistry and Chemical Biology, Cornell University Ithaca NY 14853 USA
| | - J Y Hong
- Department of Chemistry and Chemical Biology, Cornell University Ithaca NY 14853 USA
| | - M Sum
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center Breisacher Strasse 66 79106 Freiburg Germany
| | - E Metzger
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center Breisacher Strasse 66 79106 Freiburg Germany
| | - E Neuwirt
- Institute of Neuropathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg 79106 Freiburg Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg Germany
- Faculty of Biology, University of Freiburg 79104 Freiburg Germany
| | - L Zhang
- Institute of Biochemistry, University of Freiburg Albertstraße 21 79104 Freiburg Germany
| | - O Einsle
- Institute of Biochemistry, University of Freiburg Albertstraße 21 79104 Freiburg Germany
| | - O Groß
- Institute of Neuropathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg 79106 Freiburg Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg 79106 Freiburg Germany
| | - R Schüle
- Department of Urology and Center for Clinical Research, University of Freiburg Medical Center Breisacher Strasse 66 79106 Freiburg Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg Germany
| | - H Lin
- Department of Chemistry and Chemical Biology, Cornell University Ithaca NY 14853 USA
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University Ithaca NY 14853 USA
| | - W Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, University of Halle-Wittenberg Kurt-Mothes-Str. 3 06120 Halle Germany
| | - M Jung
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstraße 25 79104 Freiburg Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg Germany
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16
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Zhang J, Zou L, Shi D, Liu J, Zhang J, Zhao R, Wang G, Zhang L, Ouyang L, Liu B. Structure-Guided Design of a Small-Molecule Activator of Sirtuin-3 that Modulates Autophagy in Triple Negative Breast Cancer. J Med Chem 2021; 64:14192-14216. [PMID: 34605238 DOI: 10.1021/acs.jmedchem.0c02268] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sirtuin-3 (SIRT3) is an NAD+-dependent protein deacetylase localized primarily in the mitochondria with many links to different types of human cancers. Autophagy, which is a highly conserved lysosomal degradation process in eukaryotic cells, has been recently reported to be positively regulated by SIRT3 in cancer; therefore, activating SIRT3-modulated autophagy may be a promising strategy for drug discovery. In this study, we discovered a small-molecule activator of SIRT3 compound 33c (ADTL-SA1215) with specific SIRT3 deacetylase activity by structure-guided design and high-throughput screening. Subsequently, compound 33c inhibited the proliferation and migration of human breast carcinoma MDA-MB-231 cells by SIRT3-driven autophagy/mitophagy signaling pathways in vitro and in vivo. Collectively, these results demonstrate that pharmacological activation of SIRT3 is a potential therapeutic approach of triple negative breast cancer (TNBC). More importantly, compound 33c may be a first-in-class specific small-molecule activator of SIRT3 that would be utilized for future cancer drug development.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.,School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Ling Zou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Danfeng Shi
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.,Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Rongyan Zhao
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu, Chengdu 610031, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lan Zhang
- School of Life Science and Engineering, Southwest Jiaotong University Chengdu, Chengdu 610031, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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17
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Giardina SF, Valdambrini E, Warren JD, Barany F. PROTACs: Promising Approaches for Epigenetic Strategies to Overcome Drug Resistance. Curr Cancer Drug Targets 2021; 21:306-325. [PMID: 33535953 DOI: 10.2174/1568009621666210203110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/26/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
Epigenetic modulation of gene expression is essential for tissue-specific development and maintenance in mammalian cells. Disruption of epigenetic processes, and the subsequent alteration of gene functions, can result in inappropriate activation or inhibition of various cellular signaling pathways, leading to cancer. Recent advancements in the understanding of the role of epigenetics in cancer initiation and progression have uncovered functions for DNA methylation, histone modifications, nucleosome positioning, and non-coding RNAs. Epigenetic therapies have shown some promise for hematological malignancies, and a wide range of epigenetic-based drugs are undergoing clinical trials. However, in a dynamic survival strategy, cancer cells exploit their heterogeneous population which frequently results in the rapid acquisition of therapy resistance. Here, we describe novel approaches in drug discovery targeting the epigenome, highlighting recent advances the selective degradation of target proteins using Proteolysis Targeting Chimera (PROTAC) to address drug resistance.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
| | - Elena Valdambrini
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
| | - J David Warren
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, Box 63, New York, NY, 10065, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Ave, Box 62, New York, NY, United States
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18
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Schiedel M, Lehotzky A, Szunyogh S, Oláh J, Hammelmann S, Wössner N, Robaa D, Einsle O, Sippl W, Ovádi J, Jung M. HaloTag-Targeted Sirtuin-Rearranging Ligand (SirReal) for the Development of Proteolysis-Targeting Chimeras (PROTACs) against the Lysine Deacetylase Sirtuin 2 (Sirt2)*. Chembiochem 2020; 21:3371-3376. [PMID: 32672888 PMCID: PMC7754454 DOI: 10.1002/cbic.202000351] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/15/2020] [Indexed: 01/08/2023]
Abstract
We have discovered the sirtuin-rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+ -dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis-targeting chimera (PROTAC) enabled small-molecule-induced degradation of Sirt2. Herein, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can also be harnessed for small-molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be used as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.
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Affiliation(s)
- Matthias Schiedel
- Department of Chemistry and PharmacyMedicinal ChemistryFriedrich-Alexander-University Erlangen-NürnbergNikolaus-Fiebiger-Straße 1091058ErlangenGermany
| | - Attila Lehotzky
- Institute of EnzymologyResearch Centre for Natural SciencesMagyar Tudósok körútja 21117BudapestHungary
| | - Sandor Szunyogh
- Institute of EnzymologyResearch Centre for Natural SciencesMagyar Tudósok körútja 21117BudapestHungary
| | - Judit Oláh
- Institute of EnzymologyResearch Centre for Natural SciencesMagyar Tudósok körútja 21117BudapestHungary
| | - Sören Hammelmann
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104Freiburg im BreisgauGermany
| | - Nathalie Wössner
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104Freiburg im BreisgauGermany
| | - Dina Robaa
- Institute of PharmacyMartin-Luther-University Halle–WittenbergKurt-Mothes-Straße 306120Halle/SaaleGermany
| | - Oliver Einsle
- Institute of Biochemistry and BIOSS Centre for Biological Signalling StudiesUniversity of FreiburgAlbertstraße 2179104Freiburg im BreisgauGermany
| | - Wolfgang Sippl
- Institute of PharmacyMartin-Luther-University Halle–WittenbergKurt-Mothes-Straße 306120Halle/SaaleGermany
| | - Judit Ovádi
- Institute of EnzymologyResearch Centre for Natural SciencesMagyar Tudósok körútja 21117BudapestHungary
| | - Manfred Jung
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstraße 2579104Freiburg im BreisgauGermany
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19
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Yang W, Chen W, Su H, Li R, Song C, Wang Z, Yang L. Recent advances in the development of histone deacylase SIRT2 inhibitors. RSC Adv 2020; 10:37382-37390. [PMID: 35521274 PMCID: PMC9057128 DOI: 10.1039/d0ra06316a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Sirtuin 2 (SIRT2) is an important and special member of the atypical histone deacetylase Sirtuin (SIRT) family. Due to its extensive catalytic effects, SIRT2 can regulate autophagy, myelination, immunity, inflammation and other physiological processes. Recent evidence revealed that dysregulation of human SIRT2 activity is associated with the pathogenesis and prognosis of cancers, Parkinson's disease and other disorders; thus SIRT2 is a promising target for potential therapeutic intervention. This review presents a systematic summary of nine chemotypes of small-molecule SIRT2 inhibitors, particularly including the discovery and structural optimization strategies, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins. This review presents a systematic summarization of nine chemotypes of small-molecule SIRT2 inhibitors, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins.![]()
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Affiliation(s)
- Wenyu Yang
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Wei Chen
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Huilin Su
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Rong Li
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Chen Song
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Zhouyu Wang
- College of Science, Xihua University Sichuan 610039 China +86-28-87720552
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
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20
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Smalley JP, Cowley SM, Hodgkinson JT. Bifunctional HDAC Therapeutics: One Drug to Rule Them All? Molecules 2020; 25:E4394. [PMID: 32987782 PMCID: PMC7583022 DOI: 10.3390/molecules25194394] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylase (HDAC) enzymes play crucial roles in epigenetic gene expression and are an attractive therapeutic target. Five HDAC inhibitors have been approved for cancer treatment to date, however, clinical applications have been limited due to poor single-agent drug efficacy and side effects associated with a lack of HDAC isoform or complex selectivity. An emerging strategy aiming to address these limitations is the development of bifunctional HDAC therapeutics-single molecules comprising a HDAC inhibitor conjugated to another specificity targeting moiety. This review summarises the recent advancements in novel types of dual-targeting HDAC modulators, including proteolysis-targeting chimeras (PROTACs), with a focus on HDAC isoform and complex selectivity, and the future potential of such bifunctional molecules in achieving enhanced drug efficacy and therapeutic benefits in treating disease.
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Affiliation(s)
- Joshua P. Smalley
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, George Porter Building, University Road, Leicester LE1 7RH, UK;
| | - Shaun M. Cowley
- Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK;
| | - James T. Hodgkinson
- Leicester Institute of Structural and Chemical Biology, School of Chemistry, University of Leicester, George Porter Building, University Road, Leicester LE1 7RH, UK;
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21
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Mautone N, Zwergel C, Mai A, Rotili D. Sirtuin modulators: where are we now? A review of patents from 2015 to 2019. Expert Opin Ther Pat 2020; 30:389-407. [PMID: 32228181 DOI: 10.1080/13543776.2020.1749264] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In recent years, sirtuins (SIRTs) gained an increasing consideration because of their multiple key roles in several biological settings such as the regulation of transcription, energetic metabolism, cell cycle progression, and cytodifferentiation, apoptosis, neuro- and cardio-protection, inflammation, cancer onset and progression. Since there is mounting evidence in favor of potential therapeutic applications of SIRT modulators in various age-related disorders, the search about them is quite active. Areas covered: This review includes the patents regarding SIRT modulators released from 2015 to 2019 and provides an overview of the most relevant SIRT modulators.Expert opinion: Despite the knowledge about this family of broad-spectrum protein lysine deacylases has recently massively increased, there are still open questions, first of all, the exact nature of their involvement in various age-related conditions. The search for isoform-specific SIRT activators and inhibitors is still at its infancy, a limited number of patents describing them has been released, and not many clinical trials are ongoing. However, it is extremely likely that the successes obtained in the structural elucidation and structure-based design approaches that very recently have led to potent and specific SIRT modulators will pave the way for the development of further compounds selective for every single isoform.
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Affiliation(s)
- Nicola Mautone
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
| | - Clemens Zwergel
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy.,Dipartimento di Medicina di Precisione, "Luigi Vanvitelli", Università della Campania, Naples, Italy
| | - Antonello Mai
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
| | - Dante Rotili
- Dipartimento di Chimica e Tecnologie del Farmaco, "Sapienza" Università di Roma, Rome, Italy
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22
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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] [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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23
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Schiedel M, Daub H, Itzen A, Jung M. Validation of the Slow Off-Kinetics of Sirtuin-Rearranging Ligands (SirReals) by Means of Label-Free Electrically Switchable Nanolever Technology. Chembiochem 2020; 21:1161-1166. [PMID: 31692222 PMCID: PMC7217041 DOI: 10.1002/cbic.201900527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/31/2019] [Indexed: 12/17/2022]
Abstract
We have discovered the sirtuin-rearranging ligands (SirReals) to be highly potent and selective inhibitors of the NAD+ -dependent lysine deacetylase Sirt2. Using a biotinylated SirReal in combination with biolayer interferometry, we previously observed a slow dissociation rate of the inhibitor-enzyme complex; this had been postulated to be the key to the high affinity and selectivity of SirReals. However, to attach biotin to the SirReal core, we introduced a triazole as a linking moiety; this was shown by X-ray co-crystallography to interact with Arg97 of the cofactor binding loop. Herein, we aim to elucidate whether the observed long residence time of the SirReals is induced mainly by triazole incorporation or is an inherent characteristic of the SirReal inhibitor core. We used the novel label-free switchSENSE® technology, which is based on electrically switchable DNA nanolevers, to prove that the long residence time of the SirReals is indeed caused by the core scaffold.
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Affiliation(s)
- Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University Erlangen-Nürnberg, Nikolaus-Fiebiger-Strasse 10, 91058, Erlangen, Germany.,Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
| | - Herwin Daub
- Dynamic Biosensors GmbH, Lochhamer Strasse 15, 82152, Martinsried, Germany.,Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg im Breisgau, Germany
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24
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Wang L, Li C, Chen W, Song C, Zhang X, Yang F, Wang C, Zhang Y, Qian S, Wang Z, Yang L. Discovery of (5-Phenylfuran-2-yl)methanamine Derivatives as New Human Sirtuin 2 Inhibitors. Molecules 2019; 24:E2724. [PMID: 31357491 PMCID: PMC6695594 DOI: 10.3390/molecules24152724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/15/2019] [Accepted: 07/20/2019] [Indexed: 01/18/2023] Open
Abstract
Human sirtuin 2 (SIRT2), a member of the sirtuin family, has been considered as a promising drug target in cancer, neurodegenerative diseases, type II diabetes, and bacterial infections. Thus, SIRT2 inhibitors have been involved in effective treatment strategies for related diseases. Using previously established fluorescence-based assays for SIRT2 activity tests, the authors screened their in-house database and identified a compound, 4-(5-((3-(quinolin-5-yl)ureido)methyl)furan-2-yl)benzoic acid (20), which displayed 63 ± 5% and 35 ± 3% inhibition against SIRT2 at 100 μM and 10 μM, respectively. The structure-activity relationship (SAR) analyses of a series of synthesized (5-phenylfuran-2-yl)methanamine derivatives led to the identification of a potent compound 25 with an IC50 value of 2.47 μM, which is more potent than AGK2 (IC50 = 17.75 μM). Meanwhile, 25 likely possesses better water solubility (cLogP = 1.63 and cLogS = -3.63). Finally, the molecular docking analyses indicated that 25 fitted well with the induced hydrophobic pocket of SIRT2.
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Affiliation(s)
- Lijiao Wang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Chao Li
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Wei Chen
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Chen Song
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Xing Zhang
- College of Science, Xihua University, Sichuan 610039, China
| | - Fan Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Chen Wang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Yuanyuan Zhang
- College of Science, Xihua University, Sichuan 610039, China
| | - Shan Qian
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Zhouyu Wang
- College of Science, Xihua University, Sichuan 610039, China.
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China.
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25
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Mellini P, Itoh Y, Elboray EE, Tsumoto H, Li Y, Suzuki M, Takahashi Y, Tojo T, Kurohara T, Miyake Y, Miura Y, Kitao Y, Kotoku M, Iida T, Suzuki T. Identification of Diketopiperazine-Containing 2-Anilinobenzamides as Potent Sirtuin 2 (SIRT2)-Selective Inhibitors Targeting the "Selectivity Pocket", Substrate-Binding Site, and NAD +-Binding Site. J Med Chem 2019; 62:5844-5862. [PMID: 31144814 DOI: 10.1021/acs.jmedchem.9b00255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The NAD+-dependent deacetylase SIRT2 represents an attractive target for drug development. Here, we designed and synthesized drug-like SIRT2-selective inhibitors based on an analysis of the putative binding modes of recently reported SIRT2-selective inhibitors and evaluated their SIRT2-inhibitory activity. This led us to develop a more drug-like diketopiperazine structure as a "hydrogen bond (H-bond) hunter" to target the substrate-binding site of SIRT2. Thioamide 53, a conjugate of diketopiperazine and 2-anilinobenzamide which is expected to occupy the "selectivity pocket" of SIRT2, exhibited potent SIRT2-selective inhibition. Inhibition of SIRT2 by 53 was mediated by the formation of a 53-ADP-ribose conjugate, suggesting that 53 is a mechanism-based inhibitor targeting the "selectivity pocket", substrate-binding site, and NAD+-binding site. Furthermore, 53 showed potent antiproliferative activity toward breast cancer cells and promoted neurite outgrowth of Neuro-2a cells. These findings should pave the way for the discovery of novel therapeutic agents for cancer and neurological disorders.
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Affiliation(s)
- Paolo Mellini
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Yukihiro Itoh
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Elghareeb E Elboray
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan.,Chemistry Department, Faculty of Science , South Valley University , Qena 83523 , Egypt
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging , Tokyo Metropolitan Institute of Gerontology , 35-2 Sakae-cho , Itabashi-ku, Tokyo 173-0015 , Japan
| | - Ying Li
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Miki Suzuki
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Yukari Takahashi
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Toshifumi Tojo
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Takashi Kurohara
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Yuka Miyake
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging , Tokyo Metropolitan Institute of Gerontology , 35-2 Sakae-cho , Itabashi-ku, Tokyo 173-0015 , Japan
| | - Yuki Kitao
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Masayuki Kotoku
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Tetsuya Iida
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho , Sakyo-ku, Kyoto 606-0823 , Japan.,CREST , Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi , Saitama 332-0012 , Japan
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26
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Eren G, Bruno A, Guntekin-Ergun S, Cetin-Atalay R, Ozgencil F, Ozkan Y, Gozelle M, Kaya SG, Costantino G. Pharmacophore modeling and virtual screening studies to identify novel selective SIRT2 inhibitors. J Mol Graph Model 2019; 89:60-73. [DOI: 10.1016/j.jmgm.2019.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/15/2019] [Accepted: 02/27/2019] [Indexed: 12/12/2022]
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27
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Papatzimas JW, Gorobets E, Maity R, Muniyat MI, MacCallum JL, Neri P, Bahlis NJ, Derksen DJ. From Inhibition to Degradation: Targeting the Antiapoptotic Protein Myeloid Cell Leukemia 1 (MCL1). J Med Chem 2019; 62:5522-5540. [DOI: 10.1021/acs.jmedchem.9b00455] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- James W. Papatzimas
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
| | - Evgueni Gorobets
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
| | - Ranjan Maity
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
| | | | | | - Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
| | - Nizar J. Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
| | - Darren J. Derksen
- Arnie Charbonneau Cancer Institute, University of Calgary, 3280 Hospital Drive NW, T2N 4Z6 Calgary, Alberta, Canada
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28
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Kudo N, Ito A, Arata M, Nakata A, Yoshida M. Identification of a novel small molecule that inhibits deacetylase but not defatty-acylase reaction catalysed by SIRT2. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0070. [PMID: 29685974 DOI: 10.1098/rstb.2017.0070] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2017] [Indexed: 02/03/2023] Open
Abstract
SIRT2 is a member of the human sirtuin family of proteins and possesses NAD+-dependent lysine deacetylase/deacylase activity. SIRT2 has been implicated in carcinogenesis in various cancers including leukaemia and is considered an attractive target for cancer therapy. Here, we identified NPD11033, a selective small-molecule SIRT2 inhibitor, by a high-throughput screen using the RIKEN NPDepo chemical library. NPD11033 was largely inactive against other sirtuins and zinc-dependent deacetylases. Crystallographic analysis revealed a unique mode of action, in which NPD11033 creates a hydrophobic cavity behind the substrate-binding pocket after a conformational change of the Zn-binding small domain of SIRT2. Furthermore, it forms a hydrogen bond to the active site histidine residue. In addition, NPD11033 inhibited cell growth of human pancreatic cancer PANC-1 cells with a concomitant increase in the acetylation of eukaryotic translation initiation factor 5A, a physiological substrate of SIRT2. Importantly, NPD11033 failed to inhibit defatty-acylase activity of SIRT2, despite its potent inhibitory effect on its deacetylase activity. Thus, NPD11033 will serve as a useful tool for both developing novel anti-cancer agents and elucidating the role of SIRT2 in various cellular biological processes.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Norio Kudo
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Mayumi Arata
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akiko Nakata
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan .,Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Tokyo 113-8657, Japan
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29
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Swyter S, Schiedel M, Monaldi D, Szunyogh S, Lehotzky A, Rumpf T, Ovádi J, Sippl W, Jung M. New chemical tools for probing activity and inhibition of the NAD +-dependent lysine deacylase sirtuin 2. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0083. [PMID: 29685963 DOI: 10.1098/rstb.2017.0083] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2017] [Indexed: 01/12/2023] Open
Abstract
Sirtuins are NAD+-dependent protein deacylases capable of cleaving off acetyl as well as other acyl groups from the ɛ-amino group of lysines in histones and other substrate proteins. They have been reported as promising drug targets, and thus modulators of their activity are needed as molecular tools to uncover their biological function and as potential therapeutics. Here, we present new assay formats that complement existing assays for sirtuin biochemistry and cellular target engagement. Firstly, we report the development of a homogeneous fluorescence-based activity assay using unlabelled acylated peptides. Upon deacylation, the free lysine residue reacts with fluorescamine to form a fluorophore. Secondly, using click chemistry with a TAMRA-azide on a propargylated sirtuin inhibitor, we prepared the first fluorescently labelled small-molecule inhibitor of Sirt2. This is used in a binding assay, which is based on fluorescence polarization. We used it successfully to map potential inhibitor-binding sites and also to show cellular Sirt2 engagement. By means of these new assays, we were able to identify and characterize novel Sirt2 inhibitors out of a focused library screen. The binding of the identified Sirt2 inhibitors was rationalized by molecular docking studies. These new chemical tools thus can enhance further sirtuin research.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Sören Swyter
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany
| | - Matthias Schiedel
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Daria Monaldi
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany
| | - Sándor Szunyogh
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, 1117, Budapest, Hungary
| | - Attila Lehotzky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, 1117, Budapest, Hungary
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany.,Department of Chromatin Regulation, Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany
| | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, 1117, Budapest, Hungary
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany .,Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg, Albertstraße 19, 79104 Freiburg im Breisgau, Germany
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30
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Ali TFS, Ciftci HI, Radwan MO, Koga R, Ohsugi T, Okiyama Y, Honma T, Nakata A, Ito A, Yoshida M, Fujita M, Otsuka M. New SIRT2 inhibitors: Histidine-based bleomycin spin-off. Bioorg Med Chem 2019; 27:1767-1775. [PMID: 30885568 DOI: 10.1016/j.bmc.2019.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
Bleomycin is considered to exert its antitumor activity via DNA cleavage mediated by activated oxygen generated from the iron complex in its chelator moiety. Spin-offs from this moiety, HPH-1Trt and HPH-2Trt, with anti-cancer activities were recently synthesized. In this paper, we developed inhibitors of nicotinamide adenine dinucleotide-dependent deacetylase isoform 2 of Sirtuin protein (SIRT2), based on HPH-1Trt/HPH-2Trt, and aimed to generate new anti-cancer drugs. HPH-1Trt and HPH-2Trt had in vitro anti-SIRT2 inhibitory activity with 50% inhibitory concentration (IC50) values of 5.5 and 8.8 μM, respectively. A structural portion of HPH-1Trt/HPH-2Trt, a tritylhistidine derivative TH-1, had stronger activity (IC50 = 1.7 μM), and thus, fourteen derivatives of TH-1 were synthesized. Among them, TH-3 had the strongest activity (IC50 = 1.3 μM). Selective binding of TH-3 in the pocket of SIRT2 protein was confirmed with a molecular docking study. Furthermore, TH-3 strongly lowered viability of the breast cancer cell line MCF7 with an IC50 of 0.71 μM. A structure-activity relationship study using cell lines suggested that the mechanism of TH-3 to suppress MCF7 cells involves not only SIRT2 inhibition, but also another function. This compound may be a new candidate anti-cancer drug.
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Affiliation(s)
- Taha F S Ali
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Medicinal Chemistry Department, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
| | - Halil I Ciftci
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto 862-0976, Japan
| | - Mohamed O Radwan
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto 862-0976, Japan; Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki 12622, Cairo, Egypt
| | - Ryoko Koga
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeo Ohsugi
- Department of Laboratory Animal Science, School of Veterinary Medicine, Rakuno-Gakuen University, 582 Bunkyodai-Midorimachi, Ebetsu, Hokkaido 069-8501, Japan
| | - Yoshio Okiyama
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Teruki Honma
- Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Nakata
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Minoru Yoshida
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mikako Fujita
- Research Institute for Drug Discovery, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
| | - Masami Otsuka
- Department of Bioorganic Medicinal Chemistry, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
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31
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Ferreira GM, Magalhães JGD, Maltarollo VG, Kronenberger T, Ganesan A, Emery FDS, Trossini GHG. QSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives. J Biomol Struct Dyn 2019; 38:354-363. [PMID: 30789810 DOI: 10.1080/07391102.2019.1574603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sirtuin 2 is a key enzyme in gene expression regulation that is often associated with tumor proliferation control and therefore is a relevant anticancer drug target. Anilinobenzamide derivatives have been discussed as selective sirtuin 2 inhibitors and can be developed further. In the present study, hologram and three-dimensional quantitative structure-activity relationship (HQSAR and 3D-QSAR) analyses were employed for determining structural contributions of a compound series containing human sirtuin-2-selective inhibitors that were then correlated with structural data from the literature. The final QSAR models were robust and predictive according to statistical validation (q2 and r2pred values higher than 0.85 and 0.75, respectively) and could be employed further to generate fragment contribution and contour maps. 3D-QSAR models together with information about the chemical properties of sirtuin 2 inhibitors can be useful for designing novel bioactive ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | | | - Vinícius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
| | - Arasu Ganesan
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Flávio da Silva Emery
- Department of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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32
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D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity-Based Probe Targeting Non-Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2019; 58:1007-1012. [PMID: 30589164 PMCID: PMC6492141 DOI: 10.1002/anie.201807825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/20/2018] [Indexed: 12/27/2022]
Abstract
Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule-based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag allowed in-gel visualization and pull-down of the desired bromodomains.
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Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | | | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR)180 Massachusetts AveCambridgeMA02139USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of OxfordOxfordOX3 7DQUK
- Target Discovery Institute (TDI)University of OxfordOxfordOX3 7FZUK
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33
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D'Ascenzio M, Pugh KM, Konietzny R, Berridge G, Tallant C, Hashem S, Monteiro O, Thomas JR, Schirle M, Knapp S, Marsden B, Fedorov O, Bountra C, Kessler BM, Brennan PE. An Activity‐Based Probe Targeting Non‐Catalytic, Highly Conserved Amino Acid Residues within Bromodomains. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Melissa D'Ascenzio
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Kathryn M. Pugh
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Rebecca Konietzny
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Georgina Berridge
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Cynthia Tallant
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Shaima Hashem
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Octovia Monteiro
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Jason R. Thomas
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Markus Schirle
- Novartis Institute for BioMedical Research (NIBR) 180 Massachusetts Ave Cambridge MA 02139 USA
| | - Stefan Knapp
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University 60438 Frankfurt am Main Germany
| | - Brian Marsden
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | - Oleg Fedorov
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
| | - Chas Bountra
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
| | | | - Paul E. Brennan
- Structural Genomic Consortium (SGC)University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute (TDI)University of Oxford Oxford OX3 7FZ UK
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34
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Yang LL, Xu W, Yan J, Su HL, Yuan C, Li C, Zhang X, Yu ZJ, Yan YH, Yu Y, Chen Q, Wang Z, Li L, Qian S, Li GB. Crystallographic and SAR analyses reveal the high requirements needed to selectively and potently inhibit SIRT2 deacetylase and decanoylase. MEDCHEMCOMM 2018; 10:164-168. [PMID: 30774863 DOI: 10.1039/c8md00462e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022]
Abstract
A high-quality X-ray crystal structure reveals the mechanism of compound 1a inhibiting SIRT2 deacetylase and decanoylase. Structure-activity relationship (SAR) analysis of the synthesized derivatives of 1a reveals the high requirements needed for selective inhibitors to bind with the induced hydrophobic pocket and potently inhibit sirtuin 2 deacetylase.
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Affiliation(s)
- Ling-Ling Yang
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Wei Xu
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Jie Yan
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Hui-Lin Su
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Chen Yuan
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Chao Li
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Xing Zhang
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , Department of Medicinal Chemistry , West China School of Pharmacy , Sichuan University , Chengdu 610041 , China .
| | - Yu-Hang Yan
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , Department of Medicinal Chemistry , West China School of Pharmacy , Sichuan University , Chengdu 610041 , China .
| | - Yamei Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , Department of Medicinal Chemistry , West China School of Pharmacy , Sichuan University , Chengdu 610041 , China .
| | - Qiang Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , Department of Medicinal Chemistry , West China School of Pharmacy , Sichuan University , Chengdu 610041 , China .
| | - Zhouyu Wang
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Lin Li
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Shan Qian
- College of Food and Bioengineering , Xihua University , Sichuan 610039 , China .
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , Department of Medicinal Chemistry , West China School of Pharmacy , Sichuan University , Chengdu 610041 , China .
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An overview of Sirtuins as potential therapeutic target: Structure, function and modulators. Eur J Med Chem 2018; 161:48-77. [PMID: 30342425 DOI: 10.1016/j.ejmech.2018.10.028] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 02/05/2023]
Abstract
Sirtuin (Yeast Silent Information RegulatorsⅡ, Sir2) was first discovered in the 1970s. Because of its function by removing acetylated groups from histones in the presence of nicotinamide adenine dinucleotide (NAD+), waves of research have assessed the potential of Sirtuin as a therapeutic target. The Sirtuin family, which is widely distributed throughout the nature, has been divided into seven human isoforms (Sirt1-Sirt7). They are thought to be closely related to some aging diseases such as cardiovascular disorders, neurodegeneration, and tumors. Herein, we present a comprehensive review of the structure, function and modulators of Sirtuins, which is expected to be beneficial to relevant studies.
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36
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Schiedel M, Conway SJ. Small molecules as tools to study the chemical epigenetics of lysine acetylation. Curr Opin Chem Biol 2018; 45:166-178. [DOI: 10.1016/j.cbpa.2018.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
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37
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Yang LL, Wang HL, Zhong L, Yuan C, Liu SY, Yu ZJ, Liu S, Yan YH, Wu C, Wang Y, Wang Z, Yu Y, Chen Q, Li GB. X-ray crystal structure guided discovery of new selective, substrate-mimicking sirtuin 2 inhibitors that exhibit activities against non-small cell lung cancer cells. Eur J Med Chem 2018; 155:806-823. [DOI: 10.1016/j.ejmech.2018.06.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
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Opening the Selectivity Pocket in the Human Lysine Deacetylase Sirtuin2 – New Opportunities, New Questions. CHEM REC 2018; 18:1701-1707. [DOI: 10.1002/tcr.201800044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/06/2018] [Indexed: 12/18/2022]
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Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
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40
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Abstract
Sirtuins (SIRT) are coenzyme NAD+-dependent histone deacetylases for the transfer of modified acetyl groups. Sirtuins are widely involved in various physiological processes and therefore associated with cardiovascular disease, diabetes, Parkinson's disease, cancer and beyond. Consequently, the development of modulators for sirtuins has considerable clinical value. To date, a variety of SIRT1/2 inhibitors have been reported and none has been approved for the market. This review summarizes the recent progress in the discovery and development of SIRT1/2 inhibitors including their inhibitory potency, structure–activity relationship and binding mode analysis as well as discusses the perspective for the future development of SIRT1/2 inhibitors.
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41
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Identification of Bichalcones as Sirtuin Inhibitors by Virtual Screening and In Vitro Testing. Molecules 2018; 23:molecules23020416. [PMID: 29443909 PMCID: PMC6017733 DOI: 10.3390/molecules23020416] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 01/22/2023] Open
Abstract
Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent class III histone deacetylases, which have been linked to the pathogenesis of numerous diseases, including HIV, metabolic disorders, neurodegeneration and cancer. Docking of the virtual pan-African natural products library (p-ANAPL), followed by in vitro testing, resulted in the identification of two inhibitors of sirtuin 1, 2 and 3 (sirt1–3). Two bichalcones, known as rhuschalcone IV (8) and an analogue of rhuschalcone I (9), previously isolated from the medicinal plant Rhus pyroides, were shown to be active in the in vitro assay. The rhuschalcone I analogue (9) showed the best activity against sirt1, with an IC50 value of 40.8 µM. Based on the docking experiments, suggestions for improving the biological activities of the newly identified hit compounds have been provided.
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42
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Luise C, Robaa D. Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1. Methods Mol Biol 2018; 1824:347-370. [PMID: 30039418 DOI: 10.1007/978-1-4939-8630-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Computer-based approaches represent a powerful tool which helps to identify and optimize lead structures in the process of drug discovery. Computer-aided drug design techniques (CADD) encompass a large variety of methods which are subdivided into structure-based (SBDD) and ligand-based drug design (LBDD) methods. Several approaches have been successfully used over the last three decades in different fields. Indeed also in the field of epigenetics, virtual screening (VS) studies and structure-based approaches have been applied to identify novel chemical modulators of epigenetic targets as well as to predict the binding mode of active ligands and to study the protein dynamics.In this chapter, an iterative VS approach using both SBDD and LBDD methods, which was successful in identifying Spindlin1 inhibitors, will be described. All protocol steps, starting from structure-based pharmacophore modeling, protein and database preparation along with docking and similarity search, will be explained in details.
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Affiliation(s)
- Chiara Luise
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Martin-Luther University of Halle-Wittenberg, Halle/Saale, Germany.
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Modulation Of Microtubule Acetylation By The Interplay Of TPPP/p25, SIRT2 And New Anticancer Agents With Anti-SIRT2 Potency. Sci Rep 2017; 7:17070. [PMID: 29213065 PMCID: PMC5719079 DOI: 10.1038/s41598-017-17381-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 11/24/2017] [Indexed: 02/06/2023] Open
Abstract
The microtubule network exerts multifarious functions controlled by its decoration with various proteins and post-translational modifications. The disordered microtubule associated Tubulin Polymerization Promoting Protein (TPPP/p25) and the NAD+-dependent tubulin deacetylase sirtuin-2 (SIRT2) play key roles in oligodendrocyte differentiation by acting as dominant factors in the organization of myelin proteome. Herein, we show that SIRT2 impedes the TPPP/p25-promoted microtubule assembly independently of NAD+; however, the TPPP/p25-assembled tubulin ultrastructures were resistant against SIRT2 activity. TPPP/p25 counteracts the SIRT2-derived tubulin deacetylation producing enhanced microtubule acetylation. The inhibition of the SIRT2 deacetylase activity by TPPP/p25 is evolved by the assembly of these tubulin binding proteins into a ternary complex, the concentration-dependent formation of which was quantified by experimental-based mathematical modelling. Co-localization of the SIRT2-TPPP/p25 complex on the microtubule network was visualized in HeLa cells by immunofluorescence microscopy using Bimolecular Fluorescence Complementation. We also revealed that a new potent SIRT2 inhibitor (MZ242) and its proteolysis targeting chimera (SH1) acting together with TPPP/p25 provoke microtubule hyperacetylation, which is coupled with process elongation only in the case of the degrader SH1. Both the structural and the functional effects manifesting themselves by this deacetylase proteome could lead to the fine-tuning of the regulation of microtubule dynamics and stability.
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Mellini P, Itoh Y, Tsumoto H, Li Y, Suzuki M, Tokuda N, Kakizawa T, Miura Y, Takeuchi J, Lahtela-Kakkonen M, Suzuki T. Potent mechanism-based sirtuin-2-selective inhibition by an in situ-generated occupant of the substrate-binding site, "selectivity pocket" and NAD +-binding site. Chem Sci 2017; 8:6400-6408. [PMID: 28989670 PMCID: PMC5628579 DOI: 10.1039/c7sc02738a] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 12/19/2022] Open
Abstract
Sirtuin 2 (SIRT2), a member of the NAD+-dependent histone deacetylase family, has recently received increasing attention due to its potential involvement in neurodegenerative diseases and the progression of cancer. Potent and selective SIRT2 inhibitors thus represent desirable biological probes. Based on the X-ray crystal structure of SIRT2 in complex with a previously reported weak inhibitor (6), we identified in this study the potent mechanism-based inactivator KPM-2 (36), which is selective toward SIRT2. Compound 36 engages in a nucleophilic attack toward NAD+ at the active site of SIRT2, which affords a stable 36-ADP-ribose conjugate that simultaneously occupies the substrate-binding site, the "selectivity pocket" and the NAD+-binding site. Moreover, 36 exhibits antiproliferative activity in cancer cells and remarkable neurite outgrowth activity. This strategy for the selective inhibition of SIRT2 should allow further probing of the biology of SIRT2, and promote the development of new disease treatment strategies.
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Affiliation(s)
- Paolo Mellini
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan .
| | - Yukihiro Itoh
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan .
| | - Hiroki Tsumoto
- Research Team for Mechanism of Aging , Tokyo Metropolitan Institute of Gerontology , 35-2 Sakae-cho, Itabashi-ku , Tokyo , 173-0015 , Japan
| | - Ying Li
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan .
| | - Miki Suzuki
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan .
| | - Natsuko Tokuda
- Minase Research Institute , Ono Pharmaceutical Co., Ltd. , 3-1-1 Sakurai Shimamoto-Cho, Mishima-Gun , Osaka 618-8585 , Japan
| | - Taeko Kakizawa
- Department of Chemistry and Biochemistry , School of Advanced Science and Engineering , Waseda University , Shinjuku , Tokyo 169-8555 , Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging , Tokyo Metropolitan Institute of Gerontology , 35-2 Sakae-cho, Itabashi-ku , Tokyo , 173-0015 , Japan
| | - Jun Takeuchi
- Minase Research Institute , Ono Pharmaceutical Co., Ltd. , 3-1-1 Sakurai Shimamoto-Cho, Mishima-Gun , Osaka 618-8585 , Japan
| | - Maija Lahtela-Kakkonen
- School of Pharmacy , University of Eastern Finland , P.O. Box 1627 , 70211 Kuopio , Finland
| | - Takayoshi Suzuki
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan . .,CREST , Japan Science and Technology Agency (JST) , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
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45
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Schiedel M, Herp D, Hammelmann S, Swyter S, Lehotzky A, Robaa D, Oláh J, Ovádi J, Sippl W, Jung M. Chemically Induced Degradation of Sirtuin 2 (Sirt2) by a Proteolysis Targeting Chimera (PROTAC) Based on Sirtuin Rearranging Ligands (SirReals). J Med Chem 2017; 61:482-491. [DOI: 10.1021/acs.jmedchem.6b01872] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Matthias Schiedel
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstraße
25, 79104 Freiburg
im Breisgau, Germany
| | - Daniel Herp
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstraße
25, 79104 Freiburg
im Breisgau, Germany
| | - Sören Hammelmann
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstraße
25, 79104 Freiburg
im Breisgau, Germany
| | - Sören Swyter
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstraße
25, 79104 Freiburg
im Breisgau, Germany
| | - Attila Lehotzky
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H 1117 Budapest, Hungary
| | - Dina Robaa
- Institute
of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, 06120 Halle (Saale), Germany
| | - Judit Oláh
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H 1117 Budapest, Hungary
| | - Judit Ovádi
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja 2, H 1117 Budapest, Hungary
| | - Wolfgang Sippl
- Institute
of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstraße
25, 79104 Freiburg
im Breisgau, Germany
- Freiburg
Institute of Advanced Studies (FRIAS), University of Freiburg, Albertstraße
19, 79104 Freiburg
im Breisgau, Germany
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46
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Huang S, Song C, Wang X, Zhang G, Wang Y, Jiang X, Sun Q, Huang L, Xiang R, Hu Y, Li L, Yang S. Discovery of New SIRT2 Inhibitors by Utilizing a Consensus Docking/Scoring Strategy and Structure-Activity Relationship Analysis. J Chem Inf Model 2017; 57:669-679. [PMID: 28301150 DOI: 10.1021/acs.jcim.6b00714] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
SIRT2, which is a NAD+ (nicotinamide adenine dinucleotide) dependent deacetylase, has been demonstrated to play an important role in the occurrence and development of a variety of diseases such as cancer, ischemia-reperfusion, and neurodegenerative diseases. Small molecule inhibitors of SIRT2 are thought to be potential interfering agents for relevant diseases. Discovery of SIRT2 inhibitors has attracted much attention recently. In this investigation, we adopted a consensus docking/scoring strategy to screen for novel SIRT2 inhibitors. Structural optimization and structure-activity relationship (SAR) analysis were then carried out on highly potent compounds with new scaffolds, which led to the discovery of 2-((5-benzyl-5H-[1,2,4]triazino[5,6-b]indol-3-yl)thio)-N-(naphthalen-1-yl)acetamide (SR86). This compound showed good activity against SIRT2 with an IC50 value of 1.3 μM. SR86 did not exhibit activity against SIRT1 and SIRT3, implying a good selectivity for SIRT2. In in vitro cellular assays, SR86 displayed very good antiviability activity against breast cancer cell line MCF-7. In Western blot assays, SR86 showed considerable activity in blocking the deacetylation of α-tubulin, which is a typical substrate of SIRT2. Collectively, because of the new scaffold structure and good selectivity of SR86, it could serve as a promising lead compound, hence deserving further studies.
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Affiliation(s)
- Shenzhen Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Chunli Song
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu, Sichuan 610041, China
| | - Xiang Wang
- Department of Clinical Medicine, School of Medicine, Nankai University , Tianjin 300071, China
| | - Guo Zhang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu, Sichuan 610041, China
| | - Yanlin Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Xiaojuan Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Qizheng Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Luyi Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Rong Xiang
- Department of Clinical Medicine, School of Medicine, Nankai University , Tianjin 300071, China
| | - Yiguo Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University , Chengdu, Sichuan 610041, China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center of Biotherapy , Chengdu, Sichuan 610041, China
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47
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Sundriyal S, Moniot S, Mahmud Z, Yao S, Di Fruscia P, Reynolds CR, Dexter DT, Sternberg MJE, Lam EWF, Steegborn C, Fuchter MJ. Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket. J Med Chem 2017; 60:1928-1945. [PMID: 28135086 PMCID: PMC6014686 DOI: 10.1021/acs.jmedchem.6b01690] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 02/06/2023]
Abstract
Sirtuins (SIRTs) are NAD-dependent deacylases, known to be involved in a variety of pathophysiological processes and thus remain promising therapeutic targets for further validation. Previously, we reported a novel thienopyrimidinone SIRT2 inhibitor with good potency and excellent selectivity for SIRT2. Herein, we report an extensive SAR study of this chemical series and identify the key pharmacophoric elements and physiochemical properties that underpin the excellent activity observed. New analogues have been identified with submicromolar SIRT2 inhibtory activity and good to excellent SIRT2 subtype-selectivity. Importantly, we report a cocrystal structure of one of our compounds (29c) bound to SIRT2. This reveals our series to induce the formation of a previously reported selectivity pocket but to bind in an inverted fashion to what might be intuitively expected. We believe these findings will contribute significantly to an understanding of the mechanism of action of SIRT2 inhibitors and to the identification of refined, second generation inhibitors.
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Affiliation(s)
- Sandeep Sundriyal
- Department of Chemistry, Imperial College London, London SW7 2AZ, U.K.
| | - Sébastien Moniot
- Department of Biochemistry, University
of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
| | - Zimam Mahmud
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, U.K.
| | - Shang Yao
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, U.K.
| | - Paolo Di Fruscia
- Department of Chemistry, Imperial College London, London SW7 2AZ, U.K.
| | | | - David T. Dexter
- Centre for Neuroinflammation & Neurodegeneration,
Division of Brain Sciences, Imperial College
London, London W12 0NN, U.K.
| | | | - Eric W.-F. Lam
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, U.K.
| | - Clemens Steegborn
- Department of Biochemistry, University
of Bayreuth, Universitaetsstrasse 30, 95447 Bayreuth, Germany
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48
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Schiedel M, Robaa D, Rumpf T, Sippl W, Jung M. The Current State of NAD + -Dependent Histone Deacetylases (Sirtuins) as Novel Therapeutic Targets. Med Res Rev 2017; 38:147-200. [PMID: 28094444 DOI: 10.1002/med.21436] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 12/19/2022]
Abstract
Sirtuins are NAD+ -dependent protein deacylases that cleave off acetyl, as well as other acyl groups, from the ε-amino group of lysines in histones and other substrate proteins. Seven sirtuin isotypes (Sirt1-7) have been identified in mammalian cells. As sirtuins are involved in the regulation of various physiological processes such as cell survival, cell cycle progression, apoptosis, DNA repair, cell metabolism, and caloric restriction, a dysregulation of their enzymatic activity has been associated with the pathogenesis of neoplastic, metabolic, infectious, and neurodegenerative diseases. Thus, sirtuins are promising targets for pharmaceutical intervention. Growing interest in a modulation of sirtuin activity has prompted the discovery of several small molecules, able to inhibit or activate certain sirtuin isotypes. Herein, we give an update to our previous review on the topic in this journal (Schemies, 2010), focusing on recent developments in sirtuin biology, sirtuin modulators, and their potential as novel therapeutic agents.
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Affiliation(s)
- Matthias Schiedel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Martin-Luther Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, Martin-Luther Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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49
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Hau M, Zenk F, Ganesan A, Iovino N, Jung M. Cellular analysis of the action of epigenetic drugs and probes. Epigenetics 2017; 12:308-322. [PMID: 28071961 DOI: 10.1080/15592294.2016.1274472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small molecule drugs and probes are important tools in drug discovery, pharmacology, and cell biology. This is of course also true for epigenetic inhibitors. Important examples for the use of established epigenetic inhibitors are the study of the mechanistic role of a certain target in a cellular setting or the modulation of a certain phenotype in an approach that aims toward therapeutic application. Alternatively, cellular testing may aim at the validation of a new epigenetic inhibitor in drug discovery approaches. Cellular and eventually animal models provide powerful tools for these different approaches but certain caveats have to be recognized and taken into account. This involves both the selectivity of the pharmacological tool as well as the specificity and the robustness of the cellular system. In this article, we present an overview of different methods that are used to profile and screen for epigenetic agents and comment on their limitations. We describe not only diverse successful case studies of screening approaches using different assay formats, but also some problematic cases, critically discussing selected applications of these systems.
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Affiliation(s)
- Mirjam Hau
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany
| | - Fides Zenk
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - A Ganesan
- c School of Pharmacy, University of East Anglia , Norwich NR4 7TJ , United Kingdom.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
| | - Nicola Iovino
- b Max Planck Institute of Immunobiology and Epigenetics , Freiburg , Germany
| | - Manfred Jung
- a University of Freiburg, Institute for Pharmaceutical Sciences , Freiburg , Germany.,d Freiburg Institute of Advanced Studies (FRIAS), University of Freiburg , Freiburg , Germany
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50
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Wang HL, Liu S, Yu ZJ, Wu C, Cheng L, Wang Y, Chen K, Zhou S, Chen Q, Yu Y, Li GB. Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design. RSC Adv 2017. [DOI: 10.1039/c7ra05824a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Biophysical and crystallographic analyses of small-molecule substrates with sirtuins provide thermodynamic insights and key pharmacophore features for inhibitor design.
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Affiliation(s)
- Hua-Li Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Sha Liu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Chengyong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Linna Cheng
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Yuxi Wang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Kai Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Shu Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Qiang Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Yamei Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education
- West China School of Pharmacy, and State Key Laboratory of Biotherapy
- Sichuan University
- Chengdu
- China
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