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Yao W, Hu X, Wang X. Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases. Signal Transduct Target Ther 2024; 9:232. [PMID: 39278916 PMCID: PMC11403012 DOI: 10.1038/s41392-024-01918-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/11/2024] [Accepted: 06/30/2024] [Indexed: 09/18/2024] Open
Abstract
Histone post-translational modifications (HPTMs), as one of the core mechanisms of epigenetic regulation, are garnering increasing attention due to their close association with the onset and progression of diseases and their potential as targeted therapeutic agents. Advances in high-throughput molecular tools and the abundance of bioinformatics data have led to the discovery of novel HPTMs which similarly affect gene expression, metabolism, and chromatin structure. Furthermore, a growing body of research has demonstrated that novel histone modifications also play crucial roles in the development and progression of various diseases, including various cancers, cardiovascular diseases, infectious diseases, psychiatric disorders, and reproductive system diseases. This review defines nine novel histone modifications: lactylation, citrullination, crotonylation, succinylation, SUMOylation, propionylation, butyrylation, 2-hydroxyisobutyrylation, and 2-hydroxybutyrylation. It comprehensively introduces the modification processes of these nine novel HPTMs, their roles in transcription, replication, DNA repair and recombination, metabolism, and chromatin structure, as well as their involvement in promoting the occurrence and development of various diseases and their clinical applications as therapeutic targets and potential biomarkers. Moreover, this review provides a detailed overview of novel HPTM inhibitors targeting various targets and their emerging strategies in the treatment of multiple diseases while offering insights into their future development prospects and challenges. Additionally, we briefly introduce novel epigenetic research techniques and their applications in the field of novel HPTM research.
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Affiliation(s)
- Weiyi Yao
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China.
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, 250021, China.
- Taishan Scholars Program of Shandong Province, Jinan, Shandong, 250021, China.
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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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Wu QJ, Zhang TN, Chen HH, Yu XF, Lv JL, Liu YY, Liu YS, Zheng G, Zhao JQ, Wei YF, Guo JY, Liu FH, Chang Q, Zhang YX, Liu CG, Zhao YH. The sirtuin family in health and disease. Signal Transduct Target Ther 2022; 7:402. [PMID: 36581622 PMCID: PMC9797940 DOI: 10.1038/s41392-022-01257-8] [Citation(s) in RCA: 181] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/10/2022] [Accepted: 11/18/2022] [Indexed: 12/30/2022] Open
Abstract
Sirtuins (SIRTs) are nicotine adenine dinucleotide(+)-dependent histone deacetylases regulating critical signaling pathways in prokaryotes and eukaryotes, and are involved in numerous biological processes. Currently, seven mammalian homologs of yeast Sir2 named SIRT1 to SIRT7 have been identified. Increasing evidence has suggested the vital roles of seven members of the SIRT family in health and disease conditions. Notably, this protein family plays a variety of important roles in cellular biology such as inflammation, metabolism, oxidative stress, and apoptosis, etc., thus, it is considered a potential therapeutic target for different kinds of pathologies including cancer, cardiovascular disease, respiratory disease, and other conditions. Moreover, identification of SIRT modulators and exploring the functions of these different modulators have prompted increased efforts to discover new small molecules, which can modify SIRT activity. Furthermore, several randomized controlled trials have indicated that different interventions might affect the expression of SIRT protein in human samples, and supplementation of SIRT modulators might have diverse impact on physiological function in different participants. In this review, we introduce the history and structure of the SIRT protein family, discuss the molecular mechanisms and biological functions of seven members of the SIRT protein family, elaborate on the regulatory roles of SIRTs in human disease, summarize SIRT inhibitors and activators, and review related clinical studies.
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Affiliation(s)
- Qi-Jun Wu
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tie-Ning Zhang
- grid.412467.20000 0004 1806 3501Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Huan-Huan Chen
- grid.412467.20000 0004 1806 3501Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xue-Fei Yu
- grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jia-Le Lv
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu-Yang Liu
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ya-Shu Liu
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Gang Zheng
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jun-Qi Zhao
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi-Fan Wei
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jing-Yi Guo
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fang-Hua Liu
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Chang
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yi-Xiao Zhang
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cai-Gang Liu
- grid.412467.20000 0004 1806 3501Department of Cancer, Breast Cancer Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu-Hong Zhao
- grid.412467.20000 0004 1806 3501Liaoning Key Laboratory of Precision Medical Research on Major Chronic Disease, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, China ,grid.412467.20000 0004 1806 3501Clinical Research Center, Shengjing Hospital of China Medical University, Shenyang, China
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Abbotto E, Scarano N, Piacente F, Millo E, Cichero E, Bruzzone S. Virtual Screening in the Identification of Sirtuins’ Activity Modulators. Molecules 2022; 27:molecules27175641. [PMID: 36080416 PMCID: PMC9457788 DOI: 10.3390/molecules27175641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Sirtuins are NAD+-dependent deac(et)ylases with different subcellular localization. The sirtuins’ family is composed of seven members, named SIRT-1 to SIRT-7. Their substrates include histones and also an increasing number of different proteins. Sirtuins regulate a wide range of different processes, ranging from transcription to metabolism to genome stability. Thus, their dysregulation has been related to the pathogenesis of different diseases. In this review, we discussed the pharmacological approaches based on sirtuins’ modulators (both inhibitors and activators) that have been attempted in in vitro and/or in in vivo experimental settings, to highlight the therapeutic potential of targeting one/more specific sirtuin isoform(s) in cancer, neurodegenerative disorders and type 2 diabetes. Extensive research has already been performed to identify SIRT-1 and -2 modulators, while compounds targeting the other sirtuins have been less studied so far. Beside sections dedicated to each sirtuin, in the present review we also included sections dedicated to pan-sirtuins’ and to parasitic sirtuins’ modulators. A special focus is dedicated to the sirtuins’ modulators identified by the use of virtual screening.
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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
| | - 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
| | - Francesco Piacente
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, 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
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
- Correspondence:
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SIRT1 induces resistance to apoptosis in human granulosa cells by activating the ERK pathway and inhibiting NF-κB signaling with anti-inflammatory functions. Apoptosis 2018; 22:1260-1272. [PMID: 28755171 DOI: 10.1007/s10495-017-1386-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SIRT1, a member of the sirtuin family, has recently emerged as a vital molecule in controlling ovarian function. The aims of the present study were to investigate SIRT1 expression and analyze SIRT1-mediated apoptosis in human granulosa cells (GCs). Human ovarian tissues were subjected to immunohistochemistry for localization of SIRT1 expression. SIRT1 knockdown in a human ovarian GC tumor line (COV434) was achieved by small interfering RNA, and the relationship between apoptosis and SIRT1 was assessed by quantitative reverse transcription polymerase chain reaction and western blotting. We further detected SIRT1 expression in human luteinized GCs. Associations among SIRT1 knockdown, SIRT1 stimulation (resveratrol) and expression of ERK1/2 and apoptotic regulatory proteins were analyzed in cell lines and luteinized GCs. Resveratrol downregulated the levels of nuclear factor (NF)-κB/p65, but this inhibitory effect was attenuated by suppressing SIRT1 activity. The NF-κB/p65 inhibitor pyrrolidine dithiocarbamate achieved similar anti-apoptosis effects. These results suggest that SIRT1 might play an anti-apoptotic role in apoptosis processes in GCs, possibly by sensing and regulating the ERK1/2 pathway, which has important clinical implications. Thus, our study provides a mechanistic link, whereby activation of SIRT1 function might help to sustain human reproduction by maintaining GCs as well as oocytes, offering a novel approach for developing a new class of therapeutic anti-inflammatory agents.
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Li C, Yao J, Zhang TC, Xing W, Liang Y, Xiang M. Simultaneous removal of nitrogen and phosphorus by cetylpyridinium bromide modified zeolite. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:2895-2906. [PMID: 29210677 DOI: 10.2166/wst.2017.459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this study, surfactant modified zeolite-clinoptilolite (SMZ) by CPB (cetylpyridinium bromide) was used for simultaneous removal of ammonium, nitrate and phosphate in synthetic wastewater, and the sorption properties of SMZ were determined and compared with natural zeolite. Results showed that natural clinoptilolite had good affinity for ammonium (8.940 mg/g), but not for nitrate (0.427 mg/g) and phosphate (0.801 mg/g). With the increase of surfactant loading from 5 g/L to 40 g/L, the sorption capacity for nitrate increased from 0.462 mg/g to 4.661 mg/g. when the surfactant loading is 40 g/L, the SMZ has a phosphate adsorption capacity of 2.119 mg/g. The SMZ had a significant enhancement on nitrate and phosphate sorption, could simultaneously remove ammonium, nitrate and phosphate at specific conditions, with removal efficiency up to 85.2%, 83.1% and 56.7%, respectively. Orthogonal experiments showed that ammonium concentration was the most important factor for ammonium sorption on SMZ. Surfactant loading was the major factor for nitrate and phosphate sorption. With the increase of surfactant loading from 5 g/L to 40 g/L, the sorption capacity for nitrate increased from 0.462 mg/g to 4.661 mg/g. When the surfactant loading is 40 g/L, the SMZ has the best phosphate adsorption capacity 2.119 mg/g. Samples were characterized by X-ray diffraction (XRD) and Brunauer-Emmett-Teller (BET). Semi-empirical quantum mechanics molecular simulation indicated that electrostatic attraction existed between CPB and dihydrogen phosphate ion. Results indicate that SMZs might have great potential of removing cations and anions simultaneously in the aquatic environment, which is good for eutrophication control and nutrients removal.
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Affiliation(s)
- Chengle Li
- School of Architecture and Environmental Engineering, Sichuan University, Chengdu, 610041, China E-mail:
| | - Jing Yao
- Beijing Engineering Corporation Limited of Power China, Beijing, 100020, China
| | - Tian C Zhang
- Civil Engineering Department, University of Nebraska-Lincoln, Omaha, NE 68182-0178, USA
| | - Wenya Xing
- School of Architecture and Environmental Engineering, Sichuan University, Chengdu, 610041, China E-mail:
| | - Ying Liang
- School of Architecture and Environmental Engineering, Sichuan University, Chengdu, 610041, China E-mail: ; †These authors contributed equally to this paper
| | - Mingli Xiang
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, China; †These authors contributed equally to this paper
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Khanfar MA, Taha MO. Unsupervised pharmacophore modeling combined with QSAR analyses revealed novel low micromolar SIRT2 inhibitors. J Mol Recognit 2017; 30. [PMID: 28299833 DOI: 10.1002/jmr.2623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/18/2017] [Accepted: 02/13/2017] [Indexed: 11/10/2022]
Abstract
Situin 2 (SIRT2) enzyme is a histone deacetylase that has important role in neuronal development. SIRT2 is clinically validated target for neurodegenerative diseases and some cancers. In this study, exhaustive unsupervised pharmacophore modeling was combined with quantitative structure-activity relationship (QSAR) analysis to explore the structural requirements for potent SIRT2 inhibitors using 146 known SIRT2 ligands. A computational workflow that combines genetic function algorithm with k-nearest neighbor or multiple linear regression was implemented to build self-consistent and predictive QSAR models based on combinations of pharmacophores and physicochemical descriptors. Successful pharmacophores were complemented with exclusion spheres to optimize their receiver operating characteristic curve profiles. Optimal QSAR models and their associated pharmacophore hypotheses were experimentally validated by identification and in vitro evaluation of several new promising SIRT2 inhibitory leads retrieved from the National Cancer Institute structural database. The most potent hit illustrated IC50 value of 5.4μM. The chemical structures of active hits were validated by proton nuclear magnetic resonance and mass spectroscopy.
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Affiliation(s)
- Mohammad A Khanfar
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Univerity of Jordan, Amman, Jordan
| | - Mutasem O Taha
- Drug Discovery Unit, Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan
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Xia J, Tilahun EL, Kebede EH, Reid TE, Zhang L, Wang XS. Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families. J Chem Inf Model 2015; 55:374-88. [PMID: 25633490 DOI: 10.1021/ci5005515] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) are an important class of drug targets for the treatment of cancers, neurodegenerative diseases, and other types of diseases. Virtual screening (VS) has become fairly effective approaches for drug discovery of novel and highly selective histone deacetylase inhibitors (HDACIs). To facilitate the process, we constructed maximal unbiased benchmarking data sets for HDACs (MUBD-HDACs) using our recently published methods that were originally developed for building unbiased benchmarking sets for ligand-based virtual screening (LBVS). The MUBD-HDACs cover all four classes including Class III (Sirtuins family) and 14 HDAC isoforms, composed of 631 inhibitors and 24609 unbiased decoys. Its ligand sets have been validated extensively as chemically diverse, while the decoy sets were shown to be property-matching with ligands and maximal unbiased in terms of "artificial enrichment" and "analogue bias". We also conducted comparative studies with DUD-E and DEKOIS 2.0 sets against HDAC2 and HDAC8 targets and demonstrate that our MUBD-HDACs are unique in that they can be applied unbiasedly to both LBVS and SBVS approaches. In addition, we defined a novel metric, i.e. NLBScore, to detect the "2D bias" and "LBVS favorable" effect within the benchmarking sets. In summary, MUBD-HDACs are the only comprehensive and maximal-unbiased benchmark data sets for HDACs (including Sirtuins) that are available so far. MUBD-HDACs are freely available at http://www.xswlab.org/ .
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Affiliation(s)
- Jie Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , 38 Xueyuan Road, Beijing 100191, China
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Antagonistic crosstalk between NF-κB and SIRT1 in the regulation of inflammation and metabolic disorders. Cell Signal 2013; 25:1939-48. [DOI: 10.1016/j.cellsig.2013.06.007] [Citation(s) in RCA: 582] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 02/07/2023]
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10
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Bruzzone S, Parenti MD, Grozio A, Ballestrero A, Bauer I, Del Rio A, Nencioni A. Rejuvenating sirtuins: the rise of a new family of cancer drug targets. Curr Pharm Des 2013; 19:614-23. [PMID: 23016857 PMCID: PMC3549556 DOI: 10.2174/138161213804581954] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/25/2012] [Indexed: 01/06/2023]
Abstract
Sirtuins are a family of NAD+-dependent enzymes that was proposed to control organismal life span about a decade ago. While such role of sirtuins is now debated, mounting evidence involves these enzymes in numerous physiological processes and disease conditions, including metabolism, nutritional behavior, circadian rhythm, but also inflammation and cancer. SIRT1, SIRT2, SIRT3, SIRT6, and SIRT7 have all been linked to carcinogenesis either as tumor suppressor or as cancer promoting proteins. Here, we review the biological rationale for the search of sirtuin inhibitors and activators for treating cancer and the experimental approaches to their identification.
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Affiliation(s)
- Santina Bruzzone
- Room 221, Department of Internal Medicine, University of Genoa, V.le Benedetto XV 6, 16132 Genoa, Italy
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Disch JS, Evindar G, Chiu CH, Blum CA, Dai H, Jin L, Schuman E, Lind KE, Belyanskaya SL, Deng J, Coppo F, Aquilani L, Graybill TL, Cuozzo JW, Lavu S, Mao C, Vlasuk GP, Perni RB. Discovery of thieno[3,2-d]pyrimidine-6-carboxamides as potent inhibitors of SIRT1, SIRT2, and SIRT3. J Med Chem 2013; 56:3666-79. [PMID: 23570514 DOI: 10.1021/jm400204k] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The sirtuins SIRT1, SIRT2, and SIRT3 are NAD(+) dependent deacetylases that are considered potential targets for metabolic, inflammatory, oncologic, and neurodegenerative disorders. Encoded library technology (ELT) was used to affinity screen a 1.2 million heterocycle enriched library of DNA encoded small molecules, which identified pan-inhibitors of SIRT1/2/3 with nanomolar potency (e.g., 11c: IC50 = 3.6, 2.7, and 4.0 nM for SIRT1, SIRT2, and SIRT3, respectively). Subsequent SAR studies to improve physiochemical properties identified the potent drug like analogues 28 and 31. Crystallographic studies of 11c, 28, and 31 bound in the SIRT3 active site revealed that the common carboxamide binds in the nicotinamide C-pocket and the aliphatic portions of the inhibitors extend through the substrate channel, explaining the observable SAR. These pan SIRT1/2/3 inhibitors, representing a novel chemotype, are significantly more potent than currently available inhibitors, which makes them valuable tools for sirtuin research.
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Affiliation(s)
- Jeremy S Disch
- Sirtris a GSK Company, Cambridge, Massachusetts, United States.
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Alvala M, Bhatnagar S, Ravi A, Jeankumar VU, Manjashetty TH, Yogeeswari P, Sriram D. Novel acridinedione derivatives: design, synthesis, SIRT1 enzyme and tumor cell growth inhibition studies. Bioorg Med Chem Lett 2012; 22:3256-60. [PMID: 22464458 DOI: 10.1016/j.bmcl.2012.03.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/27/2012] [Accepted: 03/07/2012] [Indexed: 10/28/2022]
Abstract
A new scaffold N-(9-(ortho/meta/para-(benzyloxy)phenyl)-3,3,6,6-tetramethyl-1,8-dioxo-1,2,3,4,5,6,7,8-octahydroacridin-10(9H)-yl) isonicotinamide (H1-3) was discovered as a hSIRT1 inhibitor through virtual screening of in-house database. Based on these hits, a library of compounds were designed, synthesized and tested for in vitro hSIRT1 activity. The most potent compound 4d in the series showed a significant inhibition of SIRT1 activity. Further antitumor studies of compound 4d, showed a dose dependent increase in acetylation of p53K382 and decrease in SIRT1 with an IC(50) of 0.25 μM in MDA-MB231 breast cancer cell lines. Individual 3D-QSAR analysis using Schrödinger showed distribution of hydrophobic and non polar positive co-efficient at ortho position essential for bioactivity based on 4d.
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Affiliation(s)
- Mallika Alvala
- Drug Discovery Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science, Pilani-Hyderabad Campus, Hyderabad 500 078, India
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13
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Pharmacophore modeling and molecular dynamics simulation to identify the critical chemical features against human sirtuin 2 inhibitors. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.08.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Abstract
This review focuses on the progress in the development of the second generation of epigenetic modifiers able to modulate histone marks, and restore normal gene transcription.
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Affiliation(s)
- Philip Jones
- Institute for Applied Cancer Sciences
- MD Anderson Cancer Center
- Houston
- USA
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15
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Uciechowska U, Schemies J, Scharfe M, Lawson M, Wichapong K, Jung M, Sippl W. Binding free energy calculations and biological testing of novel thiobarbiturates as inhibitors of the human NAD+ dependent histone deacetylase Sirt2. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00214g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Novel thiobarbiturates were identified by virtual screening and MM-PBSA calculation as potent sirtuin inhibitors which represent useful probes for cellular studies.
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Affiliation(s)
- Urszula Uciechowska
- Department of Pharmaceutical Chemistry
- Martin-Luther Universität Halle-Wittenberg
- Halle/Saale
- Germany
| | - Jörg Schemies
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Universität
- Freiburg
- Germany
| | - Michael Scharfe
- Department of Pharmaceutical Chemistry
- Martin-Luther Universität Halle-Wittenberg
- Halle/Saale
- Germany
| | - Michael Lawson
- Department of Pharmaceutical Chemistry
- Martin-Luther Universität Halle-Wittenberg
- Halle/Saale
- Germany
| | - Kanin Wichapong
- Department of Pharmaceutical Chemistry
- Martin-Luther Universität Halle-Wittenberg
- Halle/Saale
- Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Universität
- Freiburg
- Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry
- Martin-Luther Universität Halle-Wittenberg
- Halle/Saale
- Germany
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16
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Eglen RM, Reisine T. Screening for Compounds That Modulate Epigenetic Regulation of the Transcriptome. ACTA ACUST UNITED AC 2011; 16:1137-52. [DOI: 10.1177/1087057111417871] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epigenetic control of the transciptome is a complex and highly coordinated cellular process. One critical mechanism involves DNA methylation, mediated by distinct but related DNA methyltransferases (DNMTs). Although several DNMT inhibitors are available, most are nonselective; selective DNMT inhibitors, therefore, could be optimal as therapeutics, as well acting as chemical probes to elucidate the fundamental biology of individual DNMTs. DNA methylation is a stable chemical modification, yet posttranslational modification of histones is transitory, with reversible effects on gene expression. Histone posttranslational modifications influence access of transcription factors to DNA target sites to affect gene activity. Histones are regulated by several enzymes, including acetylases (HATs), deacetylases (HDACs), methyltransferases (HMTs), and demethylases (HDMTs). Generally, HATs activate, whereas HDACs suppress gene activity. Specifically, HMTs and HDMTs can either activate or inhibit gene expression, depending on the site and extent of the methylation pattern. There is growing interest in drugs that target enzymes involved in epigenetic control. Currently, a range of high-throughput screening (HTS) technologies are used to identify selective compounds against these enzymes. This review focuses on the rationale for drug development of these enzymes, as well the utility of HTS methods used in identifying and optimizing novel selective compounds that modulate epigenetic control of the human transcriptome.
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17
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Rotili D, Carafa V, Tarantino D, Botta G, Nebbioso A, Altucci L, Mai A. Simplification of the tetracyclic SIRT1-selective inhibitor MC2141: Coumarin- and pyrimidine-based SIRT1/2 inhibitors with different selectivity profile. Bioorg Med Chem 2011; 19:3659-68. [DOI: 10.1016/j.bmc.2011.01.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 12/22/2010] [Accepted: 01/13/2011] [Indexed: 11/16/2022]
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18
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Matter H, Sotriffer C. Applications and Success Stories in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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19
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Schemies J, Uciechowska U, Sippl W, Jung M. NAD(+) -dependent histone deacetylases (sirtuins) as novel therapeutic targets. Med Res Rev 2011; 30:861-89. [PMID: 19824050 DOI: 10.1002/med.20178] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) are enzymes that cleave off acetyl groups from acetyl-lysine residues in histones and various nonhistone proteins. Four different classes of HDACs have been identified in humans so far. Although classes I, II, and IV are zinc-dependent amidohydrolases, class III HDACs depend on nicotinamide adenine dinucleotide (NAD(+)) for their catalytic activity. According to their homology to Sir2p, a yeast histone deacetylase, the class III is also termed sirtuins. Seven members have been described in humans so far. As sirtuins are involved in many physiological and pathological processes, their activity has been associated with the pathogenesis of cancer, HIV, metabolic, or neurological diseases. Herein, we present an overview over sirtuins including their biology, targets, inhibitors, and activators and their potential as new therapeutic agents.
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Affiliation(s)
- Jörg Schemies
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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20
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Computer- and structure-based lead design for epigenetic targets. Bioorg Med Chem 2011; 19:3605-15. [PMID: 21316248 DOI: 10.1016/j.bmc.2011.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 01/11/2011] [Accepted: 01/15/2011] [Indexed: 11/21/2022]
Abstract
The term epigenetics is defined as inheritable changes that influence the outcome of a phenotype without changes in the genome. Epigenetics is based upon DNA methylation and posttranslational histone modifications. While there is much known about reversible acetylation as a posttranslational modification, research on reversible histone methylation is still emerging, especially with regard to drug discovery. As aberrant epigenetic modifications have been linked to many diseases, inhibitors of histone modifying enzymes are very much in demand. This article will summarize the progress on small molecule epigenetic inhibitors identified by structure- and computer-based approaches.
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21
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Layek M, Syam Kumar Y, Islam A, Karavarapu R, Sengupta A, Halder D, Mukkanti K, Pal M. Alkynylation of N-(3-iodopyridin-2-yl)sulfonamide under Pd/C–Cu catalysis: a direct one pot synthesis of 7-azaindoles and their pharmacological evaluation as potential inhibitors of sirtuins. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00029b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Lawson M, Uciechowska U, Schemies J, Rumpf T, Jung M, Sippl W. Inhibitors to understand molecular mechanisms of NAD(+)-dependent deacetylases (sirtuins). BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:726-39. [PMID: 20601279 DOI: 10.1016/j.bbagrm.2010.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 06/08/2010] [Accepted: 06/10/2010] [Indexed: 02/01/2023]
Abstract
Histone deacetylases (HDACs) are enzymes that cleave acetyl groups from acetyl-lysine residues in histones and various nonhistone proteins. Unlike the other three of the four classes of HDACs that have been identified in humans, which are zinc-dependent amidohydrolases, class III HDACs depend on nicotinamide adenine dinucleotide (NAD(+)) for their catalytic activity. The seven members of the class III HDACs are also named sirtuins for their homology to Sir2p, a yeast histone deacetylase. Sirtuin inhibitors have been critical for the linkage of sirtuin activity to many physiological and pathological processes, and sirtuin activity has been associated with the pathogenesis of cancer, HIV, and metabolic and neurological diseases. Presented here is an overview of the many sirtuin inhibitors that have provided insight into the biological role of sirtuins.
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Affiliation(s)
- Michael Lawson
- Department of Pharmaceutical Chemistry, Martin-Luther Universität Halle-Wittenberg, Wolfgang-Langenbeckstr. 4, 06120 Halle/Saale, Germany
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23
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Huhtiniemi T, Suuronen T, Lahtela-Kakkonen M, Bruijn T, Jääskeläinen S, Poso A, Salminen A, Leppänen J, Jarho E. N(epsilon)-Modified lysine containing inhibitors for SIRT1 and SIRT2. Bioorg Med Chem 2010; 18:5616-25. [PMID: 20630764 DOI: 10.1016/j.bmc.2010.06.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/10/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
Sirtuins catalyze the NAD(+) dependent deacetylation of N(epsilon)-acetyl lysine residues to nicotinamide, O'-acetyl-ADP-ribose (OAADPR) and N(epsilon)-deacetylated lysine. Here, an easy-to-synthesize Ac-Ala-Lys-Ala sequence has been used as a probe for the screening of novel N(epsilon)-modified lysine containing inhibitors against SIRT1 and SIRT2. N(epsilon)-Selenoacetyl and N(epsilon)-isothiovaleryl were the most potent moieties found in this study, comparable to the widely studied N(epsilon)-thioacetyl group. The N(epsilon)-3,3-dimethylacryl and N(epsilon)-isovaleryl moieties gave significant inhibition in comparison to the N(epsilon)-acetyl group present in the substrates. In addition, the studied N(epsilon)-alkanoyl, N(epsilon)-alpha,beta-unsaturated carbonyl and N(epsilon)-aroyl moieties showed that the acetyl binding pocket can accept rather large groups, but is sensitive to even small changes in electronic and steric properties of the N(epsilon)-modification. These results are applicable for further screening of N(epsilon)-acetyl analogues.
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Affiliation(s)
- Tero Huhtiniemi
- School of Pharmacy, University of Eastern Finland, Kuopio Campus, PO Box 1627, 70211 Kuopio, Finland.
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24
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Sanders BD, Jackson B, Brent M, Taylor AM, Schreiber SL, Howitz K, Marmorstein R. Identification and characterization of novel sirtuin inhibitor scaffolds. Bioorg Med Chem 2009; 17:7031-41. [PMID: 19734050 PMCID: PMC2929362 DOI: 10.1016/j.bmc.2009.07.073] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 07/23/2009] [Accepted: 07/26/2009] [Indexed: 12/31/2022]
Abstract
The sirtuin proteins are broadly conserved NAD(+)-dependent deacetylases that are implicated in diverse biological processes including DNA recombination and repair, transcriptional silencing, longevity, apoptosis, axonal protection, insulin signaling, and fat mobilization. Because of these associations, the identification of small molecule sirtuin modulators has been of significant interest. Here we report on high throughput screening against the yeast sirtuin, Hst2, leading to the identification of four unique inhibitor scaffolds that also inhibit the human sirtuins, SIRT1-3, and are able to inhibit telomeric silencing of yeast Sir2 in vivo. The identified inhibitor scaffolds range in potency from IC(50) values of 6.5-130 microM against Hst2. Each of the inhibitor scaffolds binds reversibly to the enzyme, and kinetic analysis reveals that each of the inhibitors is non-competitive with respect to both acetyl-lysine and NAD(+) binding. Limited SAR analysis of the scaffolds also identifies which functional groups may be important for inhibition. These sirtuin inhibitors are low molecular weight and well-suited for lead molecule optimization, making them useful chemical probes to study the mechanism and biological roles of sirtuins and potential starting points for optimization into therapeutics.
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Affiliation(s)
- Brandi D. Sanders
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Brittany Jackson
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Michael Brent
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Alexander M. Taylor
- Howard Hughes Medical Institute, Broad Institute of Harvard and MIT, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Stuart L. Schreiber
- Howard Hughes Medical Institute, Broad Institute of Harvard and MIT, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138
| | - Konrad Howitz
- ENZO Life Sciences, Inc., 5120 Butler Pike Plymouth Meeting, PA 19462
| | - Ronen Marmorstein
- The Wistar Institute, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104 USA
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25
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Abstract
BACKGROUND The sirtuin family of deacetylase enzymes comprises seven proteins (SIRT1-7) that are dependent on NAD(+) for their activity. Three proteins are located in the nucleus, three in the mitochondria and only one is predominantly cytoplasmic. Caloric restriction and oxidative stress generally up-regulate their expression. SIRT1, the orthologue of yeast Sir2, is the mammalian sirtuin that has been most extensively studied to date. Among other targets, SIRT1 down-regulates the activity of the nuclear transcription factor p53, being this related with an increase in lifespan and cell survival associated to stress resistance. OBJECTIVE Because sirtuin modulation could have beneficial effects on several human diseases, there is a growing interest in the discovery and development of small molecules that modify its activity. This review will be focused on sirtuin inhibitors. CONCLUSIONS Several specific inhibitors of SIRT1 have been described. These compounds could be mainly useful for the treatment of cancers by increasing p53 activity that stops the formation of tumours and induces apoptosis. A p53-independent massive induction of apoptosis has been also described for one inhibitor. In addition, a potent and selective SIRT2 inhibitor that ameliorates the alpha-synuclein fibril formation in Parkinson disease has been proposed to treat this kind of neurodegenerative disease.
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Affiliation(s)
- Francisco J Alcaín
- Universidad de Córdoba, Departamento de Biología Celular, Fisiología e Inmunología, Facultad de Ciencias, Campus Rabanales, Edificio Severo Ochoa, Córdoba, Spain
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26
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Zhang Y, Au Q, Zhang M, Barber JR, Ng SC, Zhang B. Identification of a small molecule SIRT2 inhibitor with selective tumor cytotoxicity. Biochem Biophys Res Commun 2009; 386:729-33. [PMID: 19559674 DOI: 10.1016/j.bbrc.2009.06.113] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 06/21/2009] [Indexed: 12/17/2022]
Abstract
As a member of the class III histone deacetylases, Sirtuin-2 (SIRT2) is critical in cell cycle regulation which makes it a potential target for cancer therapeutics. In this study, we identified a novel SIRT2 inhibitor, AC-93253, with IC(50) of 6 microM in vitro. The compound is selective, inhibiting SIRT2 7.5- and 4-fold more potently than the closely related SIRT1 and SIRT3, respectively. AC-93253 significantly enhanced acetylation of tubulin, p53, and histone H4, confirming SIRT2 and SIRT1 as its cellular targets. AC-93253 as a single agent exhibited submicromolar selective cytotoxicity towards all four tumor cell lines tested with a therapeutic window up to 200-fold, comparing to any of the three normal cell types tested. Results from high content analysis suggested that AC-93253 significantly triggered apoptosis. Taken together, SIRT2 selective inhibitor AC-93253 may serve as a novel chemical scaffold for structure-activity relationship study and future lead development.
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Affiliation(s)
- Yingjia Zhang
- Department of Biology, CytRx Corporation, 3030 Bunker Hill Street, Suite 101, San Diego, CA 92109, USA
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27
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Amigues EJ, Armstrong E, Dvorakova M, Migaud ME, Huang M. beta-1,2,3-Triazolyl-nucleosides as nicotinamide riboside mimics. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2009; 28:238-59. [PMID: 19333861 DOI: 10.1080/15257770902865415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The synthesis of a series of pyridine- and piperidine-substituted 1,2,3-triazolides linked to a riboside moiety is described. The presence of a triazolide substituent on the pyridine moiety permitted the facile reduction of the latter under mild hydrogenation conditions. These analogues were modelled as to define their similarity to nicotinamide riboside and quantify their ability to bind NAD-dependent protein deacetylases.
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Affiliation(s)
- E J Amigues
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, Northern Ireland
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28
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Histone deacetylase inhibitors that target tubulin. Cancer Lett 2009; 280:222-32. [PMID: 19268440 DOI: 10.1016/j.canlet.2009.01.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/23/2022]
Abstract
Epigenetics is defined as heritable changes in gene expression that occur without changes in DNA sequence. Major mechanisms of epigenetics are post-translational histone modifications such as reversible acetylation. Histone deacetylases (HDACs) maintain the acetylation level of histones but also act on non-histone substrates that are involved in signal transduction or cellular transport processes. One important non-histone substrate is tubulin. The isotypes responsible for tubulin deacetylation are HDAC6 and the NAD(+)-dependent histone deacetylase (sirtuin) Sirt2. Here we review the action of those enzymes on tubulin and present an overview over existing inhibitors with a focus on their structural interaction with the targets.
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29
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Uciechowska U, Schemies J, Neugebauer RC, Huda EM, Schmitt ML, Meier R, Verdin E, Jung M, Sippl W. Thiobarbiturates as sirtuin inhibitors: virtual screening, free-energy calculations, and biological testing. ChemMedChem 2009; 3:1965-76. [PMID: 18985648 DOI: 10.1002/cmdc.200800104] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
NAD+-dependent histone deacetylases (sirtuins) are enzymes that cleave acetyl groups from lysine residues in histones and other proteins. Potent selective sirtuin inhibitors are interesting tools for the investigation of the biological functions of these enzymes and may be future drugs for the treatment of cancer or neurodegenerative diseases. Herein we present the results from a protein-based virtual screen of a commercial database with subsequent biological testing of the most promising compounds. The combination of docking and in vitro experimental testing resulted in the identification of novel sirtuin inhibitors with thiobarbiturate structure. To rationalize the experimental results, free-energy calculations were carried out by molecular mechanics Poisson-Boltzmann/surface area (MM-PBSA) calculations. A significant correlation between calculated binding free energies and measured Sirt2 inhibitory activities was observed. The analyses suggested a molecular basis for the interaction of the identified thiobarbiturate derivatives with human Sirt2. Based on the docking and MM-PBSA calculations we synthesized and tested five further thiobarbiturates. The MM-PBSA method correctly predicted the activity of the novel thiobarbiturates. The identified compounds will be used to further explore the therapeutic potential of sirtuin inhibitors.
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Affiliation(s)
- Urszula Uciechowska
- Martin-Luther Universität Halle-Wittenberg, Department of Pharmaceutical Chemistry, Wolfgang-Langenbeckstr. 4, 06120 Halle/Saale, Germany
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30
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Lead Discovery Using Virtual Screening. TOPICS IN MEDICINAL CHEMISTRY 2009. [PMCID: PMC7176223 DOI: 10.1007/7355_2009_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The practice of virtual screening (VS) to identify chemical leads to known or novel targets is becoming a core function of the computational chemist within industry. By employing a range of techniques, when attempting to identify compounds with activity against a biological target, a small focused subset of a larger collection of compounds can be identified and tested, often with results much better than selecting a similar number of compounds at random. We will review the key methods available, their relative success, and provide practical insights into best practices and key gaps. We will also argue that the capability of VS methods has grown to a point where fuller integration with experimental methods, including HTS, could increase the effectiveness of both.
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Trapp J, Meier R, Hongwiset D, Kassack MU, Sippl W, Jung M. Structure-activity studies on suramin analogues as inhibitors of NAD+-dependent histone deacetylases (sirtuins). ChemMedChem 2008; 2:1419-31. [PMID: 17628866 DOI: 10.1002/cmdc.200700003] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Suramin is a symmetric polyanionic naphthylurea originally used for the treatment of trypanosomiasis and onchocerciasis. Suramin and diverse analogues exhibit a broad range of biological actions in vitro and in vivo, including, among others, antiproliferative and antiviral activity. Suramin derivatives usually target purinergic binding sites. Class III histone deacetylases (sirtuins) are amidohydrolases that require nicotinamide adenine dinucleotide (NAD(+)) as a cofactor for their catalytic mechanism(.) Deacetylation of the target proteins leads to a change in conformation and alters the activity of the proteins in question. Suramin was reported to inhibit human sirtuin 1 (SIRT1). We tested a diverse set of suramin analogues to elucidate the inhibition of the NAD(+)-dependent histone deacetylases SIRT1 and SIRT2 and discovered selective inhibitors of human sirtuins with potency in the two-digit nanomolar range. In addition, the structural requirements for the binding of suramin derivatives to sirtuins were investigated by molecular docking. The recently published X-ray crystal structure of human SIRT5 in complex with suramin and the human SIRT2 structure were used to analyze the interaction mode of the novel suramin derivatives.
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Affiliation(s)
- Johannes Trapp
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
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32
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Kiviranta PH, Salo HS, Leppänen J, Rinne VM, Kyrylenko S, Kuusisto E, Suuronen T, Salminen A, Poso A, Lahtela-Kakkonen M, Wallén EAA. Characterization of the binding properties of SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone. Bioorg Med Chem 2008; 16:8054-62. [PMID: 18701307 DOI: 10.1016/j.bmc.2008.07.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 07/22/2008] [Indexed: 12/01/2022]
Abstract
SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone were studied. This backbone has been developed in our group, and it is derived from a compound originally found by virtual screening. In addition, compounds with a smaller 3-phenylpropenoic acid tryptamide backbone were also included in the study. Binding modes for the new compounds and the previously reported compounds were analyzed with molecular modelling methods. The approach, which included a combination of molecular dynamics, molecular docking and cluster analysis, showed that certain docking poses were favourable despite the conformational variation in the target protein. The N-(3-phenylpropenoyl)-glycine tryptamide backbone is also a good backbone for SIRT2 inhibitors, and the series of compounds includes several potent SIRT2 inhibitors.
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Affiliation(s)
- Päivi H Kiviranta
- Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland.
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Huhtiniemi T, Suuronen T, Rinne VM, Wittekindt C, Lahtela-Kakkonen M, Jarho E, Wallén EAA, Salminen A, Poso A, Leppänen J. Oxadiazole-carbonylaminothioureas as SIRT1 and SIRT2 inhibitors. J Med Chem 2008; 51:4377-80. [PMID: 18642893 DOI: 10.1021/jm800639h] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A new inhibitor for human sirtuin type proteins 1 and 2 (SIRT1 and SIRT2) was discovered through virtual database screening in search of new scaffolds. A series of compounds was synthesized based on the hit compound (3-[[3-(4-tert-butylphenyl)1,2,4-oxadiazole-5-carbonyl]amino]-1-[3-(trifluoromethyl)phenyl]thiourea). The most potent compound in the series was nearly as potent as the reference compound (6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide).
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Affiliation(s)
- Tero Huhtiniemi
- Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland.
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Neugebauer RC, Uchiechowska U, Meier R, Hruby H, Valkov V, Verdin E, Sippl W, Jung M. Structure-activity studies on splitomicin derivatives as sirtuin inhibitors and computational prediction of binding mode. J Med Chem 2008; 51:1203-13. [PMID: 18269226 DOI: 10.1021/jm700972e] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
NAD (+)-dependent histone deacetylases (sirtuins) are enzymes that cleave acetyl groups from lysines in histones and other proteins. Potent selective sirtuin inhibitors are interesting tools for the investigation of the biological functions of those enzymes and may be future drugs for the treatment of cancer. Splitomicin was among the first two inhibitors that were discovered for yeast sirtuins but showed rather weak inhibition on human enzymes. We present detailed structure-activity relationships on splitomicin derivatives and their inhibition of recombinant Sirt2. To rationalize our experimental results, ligand docking followed by molecular mechanics Poisson-Boltzmann/surface area (MM-PBSA) calculations were carried out. These analyses suggested a molecular basis for the interaction of the beta-phenylsplitomicins with human Sirt2. Protein-based virtual screening resulted in the identification of a novel Sirt2 inhibitor chemotype. Selected inhibitors showed antiproliferative properties and tubulin hyperacetylation in MCF7 breast cancer cells and are promising candidates for further optimization as potential anticancer drugs.
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Affiliation(s)
- Robert C Neugebauer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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The Sirtuin family: therapeutic targets to treat diseases of aging. Curr Opin Chem Biol 2008; 12:11-7. [DOI: 10.1016/j.cbpa.2008.01.019] [Citation(s) in RCA: 219] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 12/20/2022]
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Abstract
In contrast to genetic aberrations, epigenetic aberrations can be reversed by the use of histone acetyltransferase (HAT), histone deacetylase (HDAC), SIRT, or histone methyltransferase (HMT) inhibitors. A well-known HDACi, suberoylanilide hydroxamic acid, has been recently approved for the treatment of cutaneous T cell lymphoma, and a number of HDACi are in clinical trials as anticancer drugs. In addition, HDACi could be useful in antimalarial and antifungal therapies and can reactivate the HIV-1 expression in latent cellular reservoirs, thus suggesting the use in a combination therapy with highly active antiretroviral therapy. HDACi have also been reported to have anti-inflammatory effects through inhibition of cytokines and key transcription factors, and to ameliorate the phenotypes in animal models of neurological disorders. HDACi can also reactivate the gamma-globin gene for the treatment of beta-thalassaemia, and recently were shown to relieve morphological and functional effects of muscular dystrophia. Dysfunction of HAT enzymes is also often associated with several diseases, including cancer; thus, the HATi can represent new chemical entities for the development of new drugs. Only a few HMTi have been described to date, but these small molecules could be a useful scaffold to discovering new highly active and enzyme-selective compounds to develop as therapeutics.
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Affiliation(s)
- Antonello Mai
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Università di Roma La Sapienza, Piazzale Aldo Moro 5, I-00185 Roma, Italy.
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Kiviranta PH, Leppänen J, Rinne VM, Suuronen T, Kyrylenko O, Kyrylenko S, Kuusisto E, Tervo AJ, Järvinen T, Salminen A, Poso A, Wallén EAA. N-(3-(4-Hydroxyphenyl)-propenoyl)-amino acid tryptamides as SIRT2 inhibitors. Bioorg Med Chem Lett 2007; 17:2448-51. [PMID: 17329104 DOI: 10.1016/j.bmcl.2007.02.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
A series of N-(3-(4-hydroxyphenyl)-propenoyl)-amino acid tryptamides was based on a previously reported new SIRT2 inhibitor from our group, and it was designed to study if the molecular size of the compound could be reduced. The most potent compounds, N-(3-(4-hydroxyphenyl)-propenoyl)-2-aminoisobutyric acid tryptamide and N-(3-(4-hydroxyphenyl)-propenoyl)-L-alanine tryptamide, were equipotent, 30% smaller in molecular weight, and slightly more selective (SIRT2/SIRT1) than the parent compound.
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Affiliation(s)
- Päivi H Kiviranta
- Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland.
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