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Kaya SG, Eren G, Massarotti A, Gunindi HB, Bakar-Ates F, Ozkan E. Symmetrical 2,7-disubstituted 9H-fluoren-9-one as a novel and promising scaffold for selective targeting of SIRT2. Arch Pharm (Weinheim) 2024:e2400661. [PMID: 39340291 DOI: 10.1002/ardp.202400661] [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: 08/16/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024]
Abstract
Sirtuin 2 (SIRT2) belongs to the family of silent information regulators (sirtuins), which comprises nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacetylases. With a distribution across numerous tissues and organs of the human body, SIRT2 is involved in a wide range of physiological and pathological processes, such as regulating the cell cycle, energy metabolism, DNA repair, and tumorigenesis. Aberrant expression of SIRT2 has been closely associated with particular etiologies of human diseases, positioning SIRT2 as a promising therapeutic target. Herein, we detail the design overview and findings of novel symmetrical 2,7-disubstituted 9H-fluoren-9-one derivatives targeting SIRT2. SG3 displayed the most potent SIRT2-selective inhibitory profile, with an IC50 value of 1.95 μ M $\mu {\rm{M}}$ , and reduced the cell viability of human breast cancer MCF-7 cells accompanied by hyperacetylation of α-tubulin. Finally, molecular docking, molecular dynamics simulations, and binding free energy calculations using molecular mechanics/generalized born surface area method were performed to verify the binding ability of SG3 to SIRT2. Taken together, these results could enhance our understanding of the structural elements necessary for inhibiting SIRT2 and shed light on the mechanism of inhibition.
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Affiliation(s)
- Selen Gozde Kaya
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Türkiye
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Türkiye
| | - Alberto Massarotti
- Dipartimento di Scienze del Farmaco, Università degli Studi del Piemonte Orientale, "A. Avogadro", Novara, Italy
| | - Habibe Beyza Gunindi
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Türkiye
| | - Filiz Bakar-Ates
- Department of Biochemistry, Faculty of Pharmacy, Ankara University, Ankara, Türkiye
| | - Erva Ozkan
- Department of Biochemistry, Faculty of Pharmacy, Ankara Medipol University, Ankara, Türkiye
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2
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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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3
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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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4
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Abbotto E, Casini B, Piacente F, Scarano N, Cerri E, Tonelli M, Astigiano C, Millo E, Sturla L, Bruzzone S, Cichero E. Novel Thiazole-Based SIRT2 Inhibitors Discovered via Molecular Modelling Studies and Enzymatic Assays. Pharmaceuticals (Basel) 2023; 16:1316. [PMID: 37765125 PMCID: PMC10535842 DOI: 10.3390/ph16091316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Recently, the development of sirtuin small molecule inhibitors (SIRTIs) has been gaining attention for the treatment of different cancer types, but also to contrast neurodegenerative disease, diabetes, and autoimmune syndromes. In the search for SIRT2 modulators, the availability of several X-crystallographic data regarding SIRT2-ligand complexes has allowed for setting up a structure-based study, which is herein presented. A set of 116 SIRT2 inhibitors featuring different chemical structures has been collected from the literature and used for molecular docking studies involving 4RMG and 5MAT PDB codes. The information found highlights key contacts with the SIRT2 binding pocket such as Van der Waals and π-π stacking with Tyr104, Phe119, Phe234, and Phe235 in order to achieve high inhibitory ability values. Following the preliminary virtual screening studies, a small in-house library of compounds (1a-7a), previously investigated as putative HSP70 inhibitors, was described to guide the search for dual-acting HSP70/SIRT2 inhibitors. Biological and enzymatic assays validated the whole procedure. Compounds 2a and 7a were found to be the most promising derivatives herein proposed.
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Affiliation(s)
- Elena Abbotto
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Beatrice Casini
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
| | - Francesco Piacente
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.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; (B.C.); (N.S.); (M.T.)
| | - Elena Cerri
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Michele Tonelli
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (B.C.); (N.S.); (M.T.)
| | - Cecilia Astigiano
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Laura Sturla
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.A.); (F.P.); (E.C.); (C.A.); (E.M.); (L.S.)
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 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; (B.C.); (N.S.); (M.T.)
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Ferreira GM, Kronenberger T, Maltarollo VG, Poso A, de Moura Gatti F, Almeida VM, Marana SR, Lopes CD, Tezuka DY, de Albuquerque S, da Silva Emery F, Trossini GHG. Trypanosoma cruzi Sirtuin 2 as a Relevant Druggable Target: New Inhibitors Developed by Computer-Aided Drug Design. Pharmaceuticals (Basel) 2023; 16:ph16030428. [PMID: 36986527 PMCID: PMC10057528 DOI: 10.3390/ph16030428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, relies on finely coordinated epigenetic regulation during the transition between hosts. Herein we targeted the silent information regulator 2 (Sir2) enzyme, a NAD+-dependent class III histone deacetylase, to interfere with the parasites’ cell cycle. A combination of molecular modelling with on-target experimental validation was used to discover new inhibitors from commercially available compound libraries. We selected six inhibitors from the virtual screening, which were validated on the recombinant Sir2 enzyme. The most potent inhibitor (CDMS-01, IC50 = 40 μM) was chosen as a potential lead compound.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 17, São Paulo 05508-000, SP, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinicius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Fernando de Moura Gatti
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
| | - Vitor Medeiros Almeida
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Carla Duque Lopes
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Daiane Yukie Tezuka
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Sérgio de Albuquerque
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Flavio da Silva Emery
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
| | - Gustavo Henrique Goulart Trossini
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
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Loharch S, Chhabra S, Kumar A, Swarup S, Parkesh R. Discovery and characterization of small molecule SIRT3-specific inhibitors as revealed by mass spectrometry. Bioorg Chem 2021; 110:104768. [PMID: 33676042 DOI: 10.1016/j.bioorg.2021.104768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/20/2021] [Indexed: 01/01/2023]
Abstract
Sirtuins play a prominent role in several cellular processes and are implicated in various diseases. The understanding of biological roles of sirtuins is limited because of the non-availability of small molecule inhibitors, particularly the specific inhibitors directed against a particular SIRT. We performed a high-throughput screening of pharmacologically active compounds to discover novel, specific, and selective sirtuin inhibitor. Several unique in vitro sirtuin inhibitor pharmacophores were discovered. Here, we present the discovery of novel chemical scaffolds specific for SIRT3. We have demonstrated the in vitro activity of these compounds using label-free mass spectroscopy. We have further validated our results using biochemical, biophysical, and computational studies. Determination of kinetic parameters shows that the SIRT3 specific inhibitors have a moderately longer residence time, possibly implying high in vivo efficacy. The molecular docking results revealed the differential selectivity pattern of these inhibitors against sirtuins. The discovery of specific inhibitors will improve the understanding of ligand selectivity in sirtuins, and the binding mechanism as revealed by docking studies can be further exploited for discovering selective and potent ligands targeting sirtuins.
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Affiliation(s)
- Saurabh Loharch
- GNRPC, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Sonali Chhabra
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Abhinit Kumar
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Sapna Swarup
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Raman Parkesh
- GNRPC, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, India.
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7
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Ružić D, Đoković N, Nikolić K, Vujić Z. Medicinal chemistry of histone deacetylase inhibitors. ARHIV ZA FARMACIJU 2021. [DOI: 10.5937/arhfarm71-30618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Today, we are witnessing an explosion of scientific concepts in cancer chemotherapy. It has been considered for a long time that genetic instability in cancer should be treated with drugs that directly damage the DNA. Understanding the molecular basis of malignant diseases shed light on studying phenotypic plasticity. In the era of epigenetics, many efforts are being made to alter the aberrant homeostasis in cancer without modifying the DNA sequence. One such strategy is modulation of the lysine acetylome in human cancers. To remove the acetyl group from the histones, cells use the enzymes that are called histone deacetylases (HDACs). The disturbed equilibrium between acetylation and deacetylation on lysine residues of histones can be manipulated with histone deacetylase inhibitors (HDACi). Throughout the review, an effort will be made to present the mechanistic basis of targeting the HDAC isoforms, discovered selective HDAC inhibitors, and their therapeutical implications and expectations in modern drug discovery.
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Han H, Li C, Li M, Yang L, Zhao S, Wang Z, Liu H, Liu D. Design, Synthesis, and Biological Evaluation of 8-Mercapto-3,7-Dihydro-1 H-Purine-2,6-Diones as Potent Inhibitors of SIRT1, SIRT2, SIRT3, and SIRT5. Molecules 2020; 25:molecules25122755. [PMID: 32549218 PMCID: PMC7356367 DOI: 10.3390/molecules25122755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
Sirtuins (SIRT1-7) are a family of NAD+-dependent deacetylases. They regulate many physiological processes and play important roles in inflammation, diabetes, cancers, and neurodegeneration diseases. Sirtuin inhibitors have potential applications in the treatment of neurodegenerative diseases and various cancers. Herein, we identified new sirtuin inhibitors based on the scaffold of 8-mercapto-3,7-dihydro-1H-purine-2,6-dione. To elucidate the inhibitory mechanism, the binding modes of the inhibitors in SIRT3 were established by molecular docking, showing that the inhibitors occupy the acetyl lysine binding site and interact with SIRT3, mainly through hydrophobic interactions. The interactions were validated by site-directed mutagenesis of SIRT3 and structure-activity relationship analysis of the inhibitors. Consistently, enzyme kinetic assays and microscale thermophoresis showed that these compounds are competitive inhibitors to the acetyl substrate, and mix-type inhibitors to NAD+. Furthermore, we demonstrated that the compounds are potent SIRT1/2/3/5 pan-inhibitors. This study provides novel hits for developing more potent sirtuin inhibitors.
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Affiliation(s)
- Haozhen Han
- Department of Pharmacology III, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China;
- College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Chunpu Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China; (C.L.); (L.Y.); (S.Z.)
| | - Man Li
- School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China;
| | - Lisheng Yang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China; (C.L.); (L.Y.); (S.Z.)
| | - Sen Zhao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China; (C.L.); (L.Y.); (S.Z.)
| | - Zhifei Wang
- School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China;
- Correspondence: (Z.W.); (H.L.); (D.L.); Tel.: +86-21-50806600 (H.L. & D.L.); +86-21-51322222 (Z.W.); Fax: +86-21-50807088 (H.L.)
| | - Hong Liu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China; (C.L.); (L.Y.); (S.Z.)
- Correspondence: (Z.W.); (H.L.); (D.L.); Tel.: +86-21-50806600 (H.L. & D.L.); +86-21-51322222 (Z.W.); Fax: +86-21-50807088 (H.L.)
| | - Dongxiang Liu
- Department of Pharmacology III, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China;
- College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Correspondence: (Z.W.); (H.L.); (D.L.); Tel.: +86-21-50806600 (H.L. & D.L.); +86-21-51322222 (Z.W.); Fax: +86-21-50807088 (H.L.)
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9
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Wössner N, Alhalabi Z, González J, Swyter S, Gan J, Schmidtkunz K, Zhang L, Vaquero A, Ovaa H, Einsle O, Sippl W, Jung M. Sirtuin 1 Inhibiting Thiocyanates (S1th)-A New Class of Isotype Selective Inhibitors of NAD + Dependent Lysine Deacetylases. Front Oncol 2020; 10:657. [PMID: 32426286 PMCID: PMC7203344 DOI: 10.3389/fonc.2020.00657] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 1 (Sirt1) is a NAD+ dependent lysine deacetylase associated with the pathogenesis of various diseases including cancer. In many cancer types Sirt1 expression is increased and higher levels have been associated with metastasis and poor prognosis. However, it was also shown, that Sirt1 can have tumor suppressing properties and in some instances even a dual role for the same cancer type has been reported. Increased Sirt1 activity has been linked to extension of the life span of cells, respectively, organisms by promoting DNA repair processes and downregulation of tumor suppressor proteins. This may have the downside of enhancing tumor growth and metastasis. In mice embryonic fibroblasts depletion of Sirt1 was shown to decrease levels of the DNA damage sensor histone H2AX. Impairment of DNA repair mechanisms by Sirt1 can promote tumorigenesis but also lower chemoresistance toward DNA targeting therapies. Despite many biological studies, there is currently just one small molecule Sirt1 inhibitor in clinical trials. Selisistat (EX-527) reached phase III clinical trials for treatment of Huntington's Disease. New small molecule Sirt1 modulators are crucial for further investigation of the contradicting roles of Sirt1 in cancer. We tested a small library of commercially available compounds that were proposed by virtual screening and docking studies against Sirt1, 2 and 3. A thienopyrimidone featuring a phenyl thiocyanate moiety was found to selectively inhibit Sirt1 with an IC50 of 13 μM. Structural analogs lacking the thiocyanate function did not show inhibition of Sirt1 revealing this group as key for the selectivity and affinity toward Sirt1. Further analogs with higher solubility were identified through iterative docking studies and in vitro testing. The most active compounds (down to 5 μM IC50) were further studied in cells. The ratio of phosphorylated γH2AX to unmodified H2AX is lower when Sirt1 is depleted or inhibited. Our new Sirtuin 1 inhibiting thiocyanates (S1th) lead to similarly lowered γH2AX/H2AX ratios in mouse embryonic fibroblasts as Sirt1 knockout and treatment with the reference inhibitor EX-527. In addition to that we were able to show antiproliferative activity, inhibition of migration and colony forming as well as hyperacetylation of Sirt1 targets p53 and H3 by the S1th in cervical cancer cells (HeLa). These results reveal thiocyanates as a promising new class of selective Sirt1 inhibitors.
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Affiliation(s)
- Nathalie Wössner
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Zayan Alhalabi
- Department of Medicinal Chemistry, Institute of Pharmacy, University of Halle-Wittenberg, Halle, Germany
| | - Jessica González
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Sören Swyter
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jin Gan
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Karin Schmidtkunz
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
| | - Lin Zhang
- Department of Protein Crystallography, Institute of Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Alejandro Vaquero
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Oliver Einsle
- Department of Protein Crystallography, Institute of Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, University of Halle-Wittenberg, Halle, Germany
| | - Manfred Jung
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg im Breisgau, Germany
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10
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Krishnamoorthy V, Vilwanathan R. Silencing Sirtuin 6 induces cell cycle arrest and apoptosis in non-small cell lung cancer cell lines. Genomics 2020; 112:3703-3712. [PMID: 32360514 DOI: 10.1016/j.ygeno.2020.04.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/24/2022]
Abstract
Sirtuins (SIRT1-7), are NAD-dependent deacetylases and ADP-ribosyl transferases, plays a major part in carcinogenesis. The previous report suggests that in cancer, sirtuins gained tremendous interest and critical regulators of the unusual processes. In carcinogenesis, sirtuins possess either tumor suppressor or promoter. However, in lung cancer condition the studies of sirtuins are less studied. Hence, this designed study investigates the impact of multifaceted sirtuins in NSCLC cells. We evaluated the mRNA and protein expressions of sirtuins by RTPCR and western blot. We found SIRT6 significantly overexpressed in NCI-H520, A549, and NCI-H460 compared with the normal BEAS-2B cell line. Silencing of SIRT6 by siRNA in NSCLC cells caused activation of p53/p21 mediated inhibition of cell proliferation leading to arrest in cell cycle and apoptosis induction. Our results implied that SIRT6 is a tumor promoter in NSCLC development, progression, and regulation. The silencing of SIRT6 to be a novel therapy for lung cancer.
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Affiliation(s)
- Varunkumar Krishnamoorthy
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India.
| | - Ravikumar Vilwanathan
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620 024, India.
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11
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Liu Y, Zhang Y, Zhu K, Chi S, Wang C, Xie A. Emerging Role of Sirtuin 2 in Parkinson's Disease. Front Aging Neurosci 2020; 11:372. [PMID: 31998119 PMCID: PMC6965030 DOI: 10.3389/fnagi.2019.00372] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 12/19/2019] [Indexed: 12/17/2022] Open
Abstract
Parkinson’s disease (PD), the main risk factor of which is age, is one of the most common neurodegenerative diseases, thus presenting a substantial burden on the health of affected individuals as well as an economic burden. Sirtuin 2 (SIRT2), a subtype in the family of sirtuins, belongs to class III histone deacetylases (HDACs). It is known that SIRT2 levels increase with aging, and a growing body of evidence has been accumulating, showing that the activity of SIRT2 mediates various processes involved in PD pathogenesis, including aggregation of α-synuclein (α-syn), microtubule function, oxidative stress, inflammation, and autophagy. There have been conflicting reports about the role of SIRT2 in PD, in that some studies indicate its potential to induce the death of dopaminergic (DA) neurons, and that inhibition of SIRT2 may, therefore, have protective effects in PD. Other studies suggest a protective role of SIRT2 in the context of neuronal damage. As current treatments for PD are directed at alleviating symptoms and are very limited, a comprehensive understanding of the enzymology of SIRT2 in PD may be essential for developing novel therapeutic agents for the treatment of this disease. This review article will provide an update on our knowledge of the structure, distribution, and biological characteristics of SIRT2, and highlight its role in the pathogenesis of PD.
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Affiliation(s)
- Yumei Liu
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yingying Zhang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Konghua Zhu
- Department of Neurology, The Eighth People Hospital of Qingdao City, Qingdao, China
| | - Song Chi
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chong Wang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Anmu Xie
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
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12
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Herrera T EA, Contreras LE, Suárez AG, Diaz GJ, Ramírez MH. GlSir2.1 of Giardia lamblia is a NAD +-dependent cytoplasmic deacetylase. Heliyon 2019; 5:e01520. [PMID: 31025022 PMCID: PMC6476225 DOI: 10.1016/j.heliyon.2019.e01520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/07/2019] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
The sirtuins are a group of well-conserved proteins widely distributed across all domains of life. These proteins are clustered in the class III of histone deacetylases and are distinctly characterized by their dependence upon NAD+ to carry out the deacetylation of lysine residues in histone proteins (H3 and H4) and non-histones such as the transcription factor p53. The requirement of NAD+ for sirtuin activity makes this group of proteins metabolic sensors, which are favored during caloric stress. Currently, it is known that these proteins are involved in numerous cellular processes that are fundamental for the proper functioning of cells, including control of the cell cycle and cellular survival. In spite of the importance of sirtuins in cell functions, the role that these proteins play in protozoan parasites is not completely understood. In this study, bioinformatic modeling and experimental characterization of the candidate G1Sir2.1 present in the genome of Giardia lamblia were carried out. Consequently, cloning, expression, purification, and in vitro evaluation of the recombinant GlSir2.1 protein's capacity for deacetylation were performed. This allowed for the identification of the NAD+-dependent deacetylase activity of the identified candidate. Production of anti-rHis-GlSir2.1 polyclonal antibodies enabled the observation of a cytoplasmic localization for the endogenous protein in trophozoites, which exhibited a perinuclear aggregation and co-localization with acetylated cytoskeleton structures such as the flagella and median body. Currently, GlSir2.1 is the second sirtuin family member identified in G. lambia, with a demonstrated cytoplasmic localization in the parasite.
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Affiliation(s)
- Edian A Herrera T
- Laboratorio de Investigaciones Básicas en Bioquímica, Facultad de Ciencias, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
| | - Luis E Contreras
- Laboratorio de Investigaciones Básicas en Bioquímica, Facultad de Ciencias, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
| | - Aravy G Suárez
- Laboratorio de Investigaciones Básicas en Bioquímica, Facultad de Ciencias, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
| | - Gonzalo J Diaz
- Laboratorio de Toxicología, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
| | - María H Ramírez
- Laboratorio de Investigaciones Básicas en Bioquímica, Facultad de Ciencias, Universidad Nacional de Colombia, 111321, Bogotá, Colombia.,Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
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13
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Yuen LH, Dana S, Liu Y, Bloom SI, Thorsell AG, Neri D, Donato AJ, Kireev D, Schüler H, Franzini RM. A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes. J Am Chem Soc 2019; 141:5169-5181. [DOI: 10.1021/jacs.8b08039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Srikanta Dana
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Yu Liu
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Samuel I. Bloom
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Ann-Gerd Thorsell
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Dario Neri
- Department of Pharmaceutical Sciences, ETH Zürich, Vladimir Prelog Weg 3, 8093 Zürich, Switzerland
| | - Anthony J. Donato
- Department of Internal Medicine, University of Utah, 500 Foothill Drive, Salt Lake City, Utah 84148, United States
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Herwig Schüler
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7c, 14157 Huddinge, Sweden
| | - Raphael M. Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
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14
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Ronin C, Costa DM, Tavares J, Faria J, Ciesielski F, Ciapetti P, Smith TK, MacDougall J, Cordeiro-da-Silva A, Pemberton IK. The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design. PLoS One 2018; 13:e0193602. [PMID: 29543820 PMCID: PMC5854310 DOI: 10.1371/journal.pone.0193602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/14/2018] [Indexed: 12/21/2022] Open
Abstract
The de novo crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSir2rp1) has been solved at 1.99Å in complex with an acetyl-lysine peptide substrate. The structure is broadly commensurate with Hst2/SIRT2 proteins of yeast and human origin, reproducing many of the structural features common to these sirtuin deacetylases, including the characteristic small zinc-binding domain, and the larger Rossmann-fold domain involved in NAD+-binding interactions. The two domains are linked via a cofactor binding loop ordered in open conformation. The peptide substrate binds to the LiSir2rp1 protein via a cleft formed between the small and large domains, with the acetyl-lysine side chain inserting further into the resultant hydrophobic tunnel. Crystals were obtained only with recombinant LiSir2rp1 possessing an extensive internal deletion of a proteolytically-sensitive region unique to the sirtuins of kinetoplastid origin. Deletion of 51 internal amino acids (P253-E303) from LiSir2rp1 did not appear to alter peptide substrate interactions in deacetylation assays, but was indispensable to obtain crystals. Removal of this potentially flexible region, that otherwise extends from the classical structural elements of the Rossmann-fold, specifically the β8-β9 connector, appears to result in lower accumulation of the protein when expressed from episomal vectors in L. infantum SIR2rp1 single knockout promastigotes. The biological function of the large serine-rich insertion in kinetoplastid/trypanosomatid sirtuins, highlighted as a disordered region with strong potential for post-translational modification, remains unknown but may confer additional cellular functions that are distinct from their human counterparts. These unique molecular features, along with the resolution of the first kinetoplastid sirtuin deacetylase structure, present novel opportunities for drug design against a protein target previously established as essential to parasite survival and proliferation.
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Affiliation(s)
- Céline Ronin
- NovAliX - Bioparc, Bd Sébastien Brant, Illkirch, France
| | - David Mendes Costa
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portuga
| | - Joana Tavares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portuga
| | - Joana Faria
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portuga
| | | | | | - Terry K. Smith
- BSRC, School of Biology, University of St Andrews, St Andrews, Scotland
| | | | - Anabela Cordeiro-da-Silva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC-, Instituto de Biologia Molecular e Celular da Universidade do Porto, Porto, Portuga
- Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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15
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Song J, Yang B, Jia X, Li M, Tan W, Ma S, Shi X, Feng L. Distinctive Roles of Sirtuins on Diabetes, Protective or Detrimental? Front Endocrinol (Lausanne) 2018; 9:724. [PMID: 30559718 PMCID: PMC6284472 DOI: 10.3389/fendo.2018.00724] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/15/2018] [Indexed: 12/21/2022] Open
Abstract
Dysregulation of metabolic pathways leads to type 2 diabetes, characteristic of high glucose concentration caused by insulin resistance. The histone deacetylases sirtuins exhibit remarkable enzymatic activities. Accumulating evidence indicates that sirtuins can be pharmacologically activated to ameliorate diabetes. Here, we evaluated different roles of sirtuins (SIRT1-SIRT7) in diabetes progression and described their involvement in metabolic pathways of skeletal muscle, adipose tissue and liver. The nuclear sirtuins, SIRT1, SIRT6, and SIRT7, regulate the activity of key transcription factors and cofactors in almost all tissues with the cellular responses to energy demands. The mitochondrial sirtuins, SIRT3, SIRT4, and SIRT5, regulate the activity of mitochondrial enzymes in response to fasting and calorie restriction. Moreover, genetic polymorphisms of SIRT1 and SIRT2 have been reported to associate with diabetes development. It's worth noting that SIRT1, SIRT2, SIRT3, and SIRT6 are positive regulators of insulin resistance in most cases. In the opposite, SIRT4 and SIRT7 inhibit insulin secretion and fatty acid oxidation. Identification of SIRT1 activators for diabetes has gained wide attention, such as metformin, resveratrol, and resveratrol derivatives. Randomized, prospective, and large-scale clinical trials are warrant to uncover the responsibilities of SIRTs modulators on diabetes progress.
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Affiliation(s)
- Jie Song
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- Affiliated Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bing Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaobin Jia
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mingyu Li
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Wei Tan
- Affiliated Hospital on Integration of Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shitang Ma
- Life and Health college, Anhui Science and Technology University, Fengyang, China
| | - Xinhong Shi
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Liang Feng
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- *Correspondence: Liang Feng
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16
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Bolívar BE, Welch JT. Studies of the Binding of Modest Modulators of the Human Enzyme, Sirtuin 6, by STD NMR. Chembiochem 2017; 18:931-940. [PMID: 28222243 DOI: 10.1002/cbic.201600655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Indexed: 01/02/2023]
Abstract
Pyrazinamide (PZA), an essential constituent of short-course tuberculosis chemotherapy, binds weakly but selectively to Sirtuin 6 (SIRT6). Despite the structural similarities between nicotinamide (NAM), PZA, and pyrazinoic acid (POA), these inhibitors modulate SIRT6 by different mechanisms and through different binding sites, as suggested by saturation transfer difference (STD) NMR. Available experimental evidence, such as that derived from crystal structures and kinetic experiments, has been of only limited utility in elucidation of the mechanistic details of sirtuin inhibition by NAM or other inhibitors. For instance, crystallographic structural analysis of sirtuin binding sites does not help us understand important differences in binding affinities among sirtuins or capture details of such dynamic process. Hence, STD NMR was utilized throughout this study. Our results not only agreed with the binding kinetics experiments but also gave a qualitative insight into the binding process. The data presented herein suggested some details about the geometry of the binding epitopes of the ligands in solution with the apo- and holoenzyme. Recognition that SIRT6 is affected selectively by PZA, an established clinical agent, suggests that the rational development of more potent and selective NAM surrogates might be possible. These derivatives might be accessible by employing the malleability of this scaffold to assist in the identification by STD NMR of the motifs that interact with the apo- and holoenzymes in solution.
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Affiliation(s)
- Beatriz E Bolívar
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY, 12205, USA
| | - John T Welch
- Department of Chemistry, University at Albany, 1400 Washington Avenue, Albany, NY, 12205, USA
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17
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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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A Selective Cyclic Peptidic Human SIRT5 Inhibitor. Molecules 2016; 21:molecules21091217. [PMID: 27626398 PMCID: PMC6272981 DOI: 10.3390/molecules21091217] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022] Open
Abstract
In the current study, we discovered that a side chain-to-side chain cyclic pentapeptide harboring a central Nε-carboxyethyl-thiocarbamoyl-lysine residue behaved as a strong and selective (versus human SIRT1/2/3/6) inhibitor against human SIRT5-catalyzed deacylation reaction. This compound was also found to be proteolytically much more stable than its linear counterpart. This compound could be a valuable lead for developing stronger, selective, metabolically stable, and cell permeable human SIRT5 inhibitors.
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19
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Ai T, Wilson DJ, More SS, Xie J, Chen L. 5-((3-Amidobenzyl)oxy)nicotinamides as Sirtuin 2 Inhibitors. J Med Chem 2016; 59:2928-41. [PMID: 26982234 DOI: 10.1021/acs.jmedchem.5b01376] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Derived from our previously reported human sirtuin 2 (SIRT2) inhibitors that were based on a 5-aminonaphthalen-1-yloxy nicotinamide core structure, 5-((3-amidobenzyl)oxy)nicotinamides offered excellent activity against SIRT2 and high isozyme selectivity over SIRT1 and SIRT3. Selected compounds also exhibited generally favorable in vitro absorption, distribution, metabolism, and excretion properties. Kinetic studies revealed that a representative SIRT2 inhibitor acted competitively against both NAD(+) and the peptide substrate, an inhibitory modality that was supported by our computational study. More importantly, two selected compounds exhibited significant protection against α-synuclein aggregation-induced cytotoxicity in SH-SY5Y cells. Therefore, 5-((3-amidobenzyl)oxy)nicotinamides represent a new class of SIRT2 inhibitors that are attractive candidates for further lead optimization in our continued effort to explore selective inhibition of SIRT2 as a potential therapy for Parkinson's disease.
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Affiliation(s)
- Teng Ai
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Swati S More
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
| | - Liqiang Chen
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
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20
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Huang Y, Liu J, Yan L, Zheng W. Simple N ε -thioacetyl-lysine-containing cyclic peptides exhibiting highly potent sirtuin inhibition. Bioorg Med Chem Lett 2016; 26:1612-1617. [DOI: 10.1016/j.bmcl.2016.01.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/26/2016] [Accepted: 01/30/2016] [Indexed: 01/05/2023]
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21
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Sociali G, Galeno L, Parenti MD, Grozio A, Bauer I, Passalacqua M, Boero S, Donadini A, Millo E, Bellotti M, Sturla L, Damonte P, Puddu A, Ferroni C, Varchi G, Franceschi C, Ballestrero A, Poggi A, Bruzzone S, Nencioni A, Del Rio A. Quinazolinedione SIRT6 inhibitors sensitize cancer cells to chemotherapeutics. Eur J Med Chem 2015; 102:530-9. [PMID: 26310895 DOI: 10.1016/j.ejmech.2015.08.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 01/09/2023]
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22
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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