1
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Tuo Y, Tang Y, Yang R, Zhao X, Luo M, Zhou X, Wang Y. Virtual screening and biological activity evaluation of novel efflux pump inhibitors targeting AdeB. Int J Biol Macromol 2023; 250:126109. [PMID: 37544561 DOI: 10.1016/j.ijbiomac.2023.126109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
The AdeABC efflux pump is an important mechanism causing multidrug resistance in Acinetobacter baumannii, and its main component AdeB can recognize carbapenems, aminoglycosides, and other multi-class antibiotics and efflux them intracellularly, which is an ideal target for the development of anti-multidrug resistant bacteria drugs. Here, we combined multiple computer-aided drug design methods to target AdeB to identify promising novel structural inhibitors. Virtual screening was performed by molecular docking and molecular dynamics simulation (MD) and 12 potential compounds were identified from the databases. Meanwhile, their biological activities were validated by in vitro activity assays, and ChemDiv L676-2179 (γ-IFN), ChemDiv L676-1461, and Chembridge 53717615 were confirmed to suppress efflux effects and restore antibiotic susceptibility of resistant bacteria, which are expected to be developed as adjuvant drugs for the treatment of multi-drug resistant Acinetobacter baumannii clinical infections.
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Affiliation(s)
- Yan Tuo
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yuelu Tang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ran Yang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - XueMin Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Minghe Luo
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xing Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China; Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China; Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China.
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2
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Scarano N, Abbotto E, Musumeci F, Salis A, Brullo C, Fossa P, Schenone S, Bruzzone S, Cichero E. Virtual Screening Combined with Enzymatic Assays to Guide the Discovery of Novel SIRT2 Inhibitors. Int J Mol Sci 2023; 24:ijms24119363. [PMID: 37298312 DOI: 10.3390/ijms24119363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Sirtuin isoform 2 (SIRT2) is one of the seven sirtuin isoforms present in humans, being classified as class III histone deacetylases (HDACs). Based on the high sequence similarity among SIRTs, the identification of isoform selective modulators represents a challenging task, especially for the high conservation observed in the catalytic site. Efforts in rationalizing selectivity based on key residues belonging to the SIRT2 enzyme were accompanied in 2015 by the publication of the first X-ray crystallographic structure of the potent and selective SIRT2 inhibitor SirReal2. The subsequent studies led to different experimental data regarding this protein in complex with further different chemo-types as SIRT2 inhibitors. Herein, we reported preliminary Structure-Based Virtual Screening (SBVS) studies using a commercially available library of compounds to identify novel scaffolds for the design of new SIRT2 inhibitors. Biochemical assays involving five selected compounds allowed us to highlight the most effective chemical features supporting the observed SIRT2 inhibitory ability. This information guided the following in silico evaluation and in vitro testing of further compounds from in-house libraries of pyrazolo-pyrimidine derivatives towards novel SIRT2 inhibitors (1-5). The final results indicated the effectiveness of this scaffold for the design of promising and selective SIRT2 inhibitors, featuring the highest inhibition among the tested compounds, and validating the applied strategy.
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Affiliation(s)
- Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Elena Abbotto
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Francesca Musumeci
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Annalisa Salis
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Paola Fossa
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Silvia Schenone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy
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3
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Ahamad S, Bhat SA. The Emerging Landscape of Small-Molecule Therapeutics for the Treatment of Huntington's Disease. J Med Chem 2022; 65:15993-16032. [PMID: 36490325 DOI: 10.1021/acs.jmedchem.2c00799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). The new insights into HD's cellular and molecular pathways have led to the identification of numerous potent small-molecule therapeutics for HD therapy. The field of HD-targeting small-molecule therapeutics is accelerating, and the approval of these therapeutics to combat HD may be expected in the near future. For instance, preclinical candidates such as naphthyridine-azaquinolone, AN1, AN2, CHDI-00484077, PRE084, EVP4593, and LOC14 have shown promise for further optimization to enter into HD clinical trials. This perspective aims to summarize the advent of small-molecule therapeutics at various stages of clinical development for HD therapy, emphasizing their structure and design, therapeutic effects, and specific mechanisms of action. Further, we have highlighted the key drivers involved in HD pathogenesis to provide insights into the basic principle for designing promising anti-HD therapeutic leads.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
| | - Shahnawaz A Bhat
- Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh202002, India
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4
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Manjula R, Anuja K, Alcain FJ. SIRT1 and SIRT2 Activity Control in Neurodegenerative Diseases. Front Pharmacol 2021; 11:585821. [PMID: 33597872 PMCID: PMC7883599 DOI: 10.3389/fphar.2020.585821] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
Sirtuins are NAD+ dependent histone deacetylases (HDAC) that play a pivotal role in neuroprotection and cellular senescence. SIRT1-7 are different homologs from sirtuins. They play a prominent role in many aspects of physiology and regulate crucial proteins. Modulation of sirtuins can thus be utilized as a therapeutic target for metabolic disorders. Neurological diseases have distinct clinical manifestations but are mainly age-associated and due to loss of protein homeostasis. Sirtuins mediate several life extension pathways and brain functions that may allow therapeutic intervention for age-related diseases. There is compelling evidence to support the fact that SIRT1 and SIRT2 are shuttled between the nucleus and cytoplasm and perform context-dependent functions in neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). In this review, we highlight the regulation of SIRT1 and SIRT2 in various neurological diseases. This study explores the various modulators that regulate the activity of SIRT1 and SIRT2, which may further assist in the treatment of neurodegenerative disease. Moreover, we analyze the structure and function of various small molecules that have potential significance in modulating sirtuins, as well as the technologies that advance the targeted therapy of neurodegenerative disease.
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Affiliation(s)
- Ramu Manjula
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, United States
| | - Kumari Anuja
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Francisco J. Alcain
- Department of Medical Sciences, Faculty of Medicine, University of Castilla-La Mancha, Albacete, Spain
- Oxidative Stress and Neurodegeneration Group, Regional Center for Biomedical Research, University of Castilla-La Mancha, Ciudad Real, Spain
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5
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Yang W, Chen W, Su H, Li R, Song C, Wang Z, Yang L. Recent advances in the development of histone deacylase SIRT2 inhibitors. RSC Adv 2020; 10:37382-37390. [PMID: 35521274 PMCID: PMC9057128 DOI: 10.1039/d0ra06316a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Sirtuin 2 (SIRT2) is an important and special member of the atypical histone deacetylase Sirtuin (SIRT) family. Due to its extensive catalytic effects, SIRT2 can regulate autophagy, myelination, immunity, inflammation and other physiological processes. Recent evidence revealed that dysregulation of human SIRT2 activity is associated with the pathogenesis and prognosis of cancers, Parkinson's disease and other disorders; thus SIRT2 is a promising target for potential therapeutic intervention. This review presents a systematic summary of nine chemotypes of small-molecule SIRT2 inhibitors, particularly including the discovery and structural optimization strategies, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins. This review presents a systematic summarization of nine chemotypes of small-molecule SIRT2 inhibitors, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins.![]()
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Affiliation(s)
- Wenyu Yang
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Wei Chen
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Huilin Su
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Rong Li
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Chen Song
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
| | - Zhouyu Wang
- College of Science, Xihua University Sichuan 610039 China +86-28-87720552
| | - Lingling Yang
- College of Food and Bioengineering, Xihua University Chengdu 610039 China
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6
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Eren G, Bruno A, Guntekin-Ergun S, Cetin-Atalay R, Ozgencil F, Ozkan Y, Gozelle M, Kaya SG, Costantino G. Pharmacophore modeling and virtual screening studies to identify novel selective SIRT2 inhibitors. J Mol Graph Model 2019; 89:60-73. [DOI: 10.1016/j.jmgm.2019.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/15/2019] [Accepted: 02/27/2019] [Indexed: 12/12/2022]
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7
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Martinez-Quiroz M, Aguilar-Martinez XE, Oropeza-Guzman MT, Valdez R, Lopez-Maldonado EA. Evaluation of N-Alkyl-bis- o-aminobenzamide Receptors for the Determination and Separation of Metal Ions by Fluorescence, UV-Visible Spectrometry and Zeta Potential. Molecules 2019; 24:molecules24091737. [PMID: 31060217 PMCID: PMC6539274 DOI: 10.3390/molecules24091737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/13/2019] [Accepted: 04/13/2019] [Indexed: 11/16/2022] Open
Abstract
This paper presents the synthesis and evaluation of physicochemical behavior of a new series of N-alkyl-bis-o-aminobenzamides (BOABs) in aqueous solution. The study was targeted to the complexing capacity of five metal ions (Fe2+, Cu2+, Cd2+, Hg2+ and Pb2+) of environmental concern as the medullar principle of a liquid phase sensor for its application in the determination of these metal ions due to its versatility of use. Molecular fluorescence, UV-visible and Zeta potential were measured for five BOABs and the effect of alkyl groups with different central chain length (n = 3, 4, 6, 8 and 10) on physicochemical performance determined. The results have shown that these derivatives present higher sensibility and selectivity for Cu2+ even in the presence of the other metal ions. An additional application test was done adding a pectin (0.1 wt %) solution to the BOAB-Cu+2 complex to obtain a precipitate (flocs) as a potential selective separation process of Cu from aqueous solution. The solid was then lyophilized and analyzed by SEM-EDS, the images showed spheric forms containing Cu+2 with diameter of approximately of 8 μm and 30 wt %.
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Affiliation(s)
- Marisela Martinez-Quiroz
- CETYS Universidad, Centro de Innovación y Diseño, Escuela de Ingenieria Av. CETYS Universidad No. 4 Fracc. El Lago, Tijuana, B.C. CP 22210, México.
- Tecnologico Nacional de México, Instituto Tecnológico de Tijuana, Blvd. Alberto Limón Padilla s/n, Mesa de Otay, Tijuana, B.C. CP 22500, México.
| | - Xiomara E Aguilar-Martinez
- Tecnologico Nacional de México, Instituto Tecnológico de Tijuana, Blvd. Alberto Limón Padilla s/n, Mesa de Otay, Tijuana, B.C. CP 22500, México.
| | - Mercedes T Oropeza-Guzman
- Tecnologico Nacional de México, Instituto Tecnológico de Tijuana, Blvd. Alberto Limón Padilla s/n, Mesa de Otay, Tijuana, B.C. CP 22500, México.
| | - Ricardo Valdez
- Centro de Nanociencias y Nanotecnología CNyN-UNAM, Km 107 Carretera Tijuana-Ensenada, Ensenada, B.C. CP 22860, México.
| | - Eduardo A Lopez-Maldonado
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana, B.C. CP 22390, México.
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8
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Veale CGL. Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease. ChemMedChem 2019; 14:386-453. [PMID: 30614200 DOI: 10.1002/cmdc.201800755] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 12/13/2022]
Abstract
The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
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9
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Zha GF, Rakesh K, Manukumar H, Shantharam C, Long S. Pharmaceutical significance of azepane based motifs for drug discovery: A critical review. Eur J Med Chem 2019; 162:465-494. [DOI: 10.1016/j.ejmech.2018.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/13/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
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10
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An overview of Sirtuins as potential therapeutic target: Structure, function and modulators. Eur J Med Chem 2018; 161:48-77. [PMID: 30342425 DOI: 10.1016/j.ejmech.2018.10.028] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 02/05/2023]
Abstract
Sirtuin (Yeast Silent Information RegulatorsⅡ, Sir2) was first discovered in the 1970s. Because of its function by removing acetylated groups from histones in the presence of nicotinamide adenine dinucleotide (NAD+), waves of research have assessed the potential of Sirtuin as a therapeutic target. The Sirtuin family, which is widely distributed throughout the nature, has been divided into seven human isoforms (Sirt1-Sirt7). They are thought to be closely related to some aging diseases such as cardiovascular disorders, neurodegeneration, and tumors. Herein, we present a comprehensive review of the structure, function and modulators of Sirtuins, which is expected to be beneficial to relevant studies.
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11
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Zhao J, Niu S, Jiang X, Jiang Y, Zhang X, Sun T, Ma D. A Class of Amide Ligands Enable Cu-Catalyzed Coupling of (Hetero)aryl Halides with Sulfinic Acid Salts under Mild Conditions. J Org Chem 2018; 83:6589-6598. [DOI: 10.1021/acs.joc.8b00888] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jinlong Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Songtao Niu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Xi Jiang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Yongwen Jiang
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Xiaojing Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, China
| | - Dawei Ma
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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12
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The Fungal Metabolite Eurochevalierine, a Sequiterpene Alkaloid, Displays Anti-Cancer Properties through Selective Sirtuin 1/2 Inhibition. Molecules 2018; 23:molecules23020333. [PMID: 29401749 PMCID: PMC6017873 DOI: 10.3390/molecules23020333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/19/2023] Open
Abstract
NAD+-dependent histone deacetylases (sirtuins) are implicated in cellular processes such as proliferation, DNA repair, and apoptosis by regulating gene expression and the functions of numerous proteins. Due to their key role in cells, the discovery of small molecule sirtuin modulators has been of significant interest for diverse therapeutic applications. In particular, it has been shown that inhibition of sirtuin 1 and 2 activities is beneficial for cancer treatment. Here, we demonstrate that the fungal metabolite eurochevalierine from the fungus Neosartorya pseudofischeri inhibits sirtuin 1 and 2 activities (IC50 about 10 µM) without affecting sirtuin 3 activity. The binding modes of the eurochevalierine for sirtuin 1 and 2 have been identified through computational docking analyses. Accordingly, this sequiterpene alkaloid induces histone H4 and α-tubulin acetylation in various cancer cell models in which it induces strong cytostatic effects without affecting significantly the viability of healthy PBMCs. Importantly, eurochevalierine targets preferentially cancer cell proliferation (selectivity factor ≫ 7), as normal human primary CD34+ stem/progenitor cells were less affected by the treatment. Finally, eurochevalierine displays suitable drug-likeness parameters and therefore represent a promising scaffold for lead molecule optimization to study the mechanism and biological roles of sirtuins and potentially a basis for development into therapeutics.
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13
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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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14
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Verlee A, Heugebaert T, van der Meer T, Kerchev PI, Van Breusegem F, Stevens CV. A chemoselective and continuous synthesis of m-sulfamoylbenzamide analogues. Beilstein J Org Chem 2017; 13:303-312. [PMID: 28326139 PMCID: PMC5331323 DOI: 10.3762/bjoc.13.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 02/03/2017] [Indexed: 11/23/2022] Open
Abstract
For the synthesis of m-sulfamoylbenzamide analogues, small molecules which are known for their bioactivity, a chemoselective procedure has been developed starting from m-(chlorosulfonyl)benzoyl chloride. Although a chemoselective process in batch was already reported, a continuous-flow process reveals an increased selectivity at higher temperatures and without catalysts. In total, 15 analogues were synthesized, using similar conditions, with yields ranging between 65 and 99%. This is the first automated and chemoselective synthesis of m-sulfamoylbenzamide analogues.
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Affiliation(s)
- Arno Verlee
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, Coupure Links 653, B-9000 Ghent, Belgium
| | - Thomas Heugebaert
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tom van der Meer
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Pavel I Kerchev
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
| | - Christian V Stevens
- Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, Coupure Links 653, B-9000 Ghent, Belgium
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15
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Yu Z, Xie X, Dong H, Liu J, Su W. Continuous-Flow Process for the Synthesis of m-Nitrothioanisole. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiqun Yu
- National
Engineering Research Center for Process Development of Active Pharmaceutical
Ingredients, Collaborative Innovation Center of Yangtze River Delta
Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Xiaoxuan Xie
- National
Engineering Research Center for Process Development of Active Pharmaceutical
Ingredients, Collaborative Innovation Center of Yangtze River Delta
Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Hei Dong
- National
Engineering Research Center for Process Development of Active Pharmaceutical
Ingredients, Collaborative Innovation Center of Yangtze River Delta
Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Jiming Liu
- Key
Laboratory for Green Pharmaceutical Technologies and Related Equipment
of Ministry of Education, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Weike Su
- National
Engineering Research Center for Process Development of Active Pharmaceutical
Ingredients, Collaborative Innovation Center of Yangtze River Delta
Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- Key
Laboratory for Green Pharmaceutical Technologies and Related Equipment
of Ministry of Education, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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16
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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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17
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Naia L, Rego AC. Sirtuins: double players in Huntington's disease. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2183-94. [DOI: 10.1016/j.bbadis.2015.07.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 11/16/2022]
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18
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Khanfar MA, Quinti L, Wang H, Nobles J, Kazantsev AG, Silverman RB. Design and Evaluation of 3-(Benzylthio)benzamide Derivatives as Potent and Selective SIRT2 Inhibitors. ACS Med Chem Lett 2015; 6:607-11. [PMID: 26005542 DOI: 10.1021/acsmedchemlett.5b00075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/26/2015] [Indexed: 01/06/2023] Open
Abstract
Inhibitors of sirtuin-2 (SIRT2) deacetylase have been shown to be protective in various models of Huntington's disease (HD) by decreasing polyglutamine aggregation, a hallmark of HD pathology. The present study was directed at optimizing the potency of SIRT2 inhibitors containing the 3-(benzylsulfonamido)benzamide scaffold and improving their metabolic stability. Molecular modeling and docking studies revealed an unfavorable role of the sulfonamide moiety for SIRT2 binding. This prompted us to replace the sulfonamide with thioether, sulfoxide, or sulfone groups. The thioether analogues were the most potent SIRT2 inhibitors with a two- to three-fold increase in potency relative to their corresponding sulfonamide analogues. The newly synthesized compounds also demonstrated higher SIRT2 selectivity over SIRT1 and SIRT3. Two thioether-derived compounds (17 and 18) increased α-tubulin acetylation in a dose-dependent manner in at least one neuronal cell line, and 18 was found to inhibit polyglutamine aggregation in PC12 cells.
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Affiliation(s)
- Mohammad A. Khanfar
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
- Department
of Pharmaceutical Sciences, The University of Jordan, Amman, Jordan
| | - Luisa Quinti
- Department
of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, Massachusetts 02129-4404, United States
| | - Hua Wang
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Johnathan Nobles
- Department
of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, Massachusetts 02129-4404, United States
| | - Aleksey G. Kazantsev
- Department
of Neurology, Harvard Medical School and Massachusetts General Hospital, Charlestown, Massachusetts 02129-4404, United States
| | - Richard B. Silverman
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208-3113, United States
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19
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Cai J, Wei H, Hong KH, Wu X, Cao M, Zong X, Li L, Sun C, Chen J, Ji M. Discovery and preliminary evaluation of 2-aminobenzamide and hydroxamate derivatives containing 1,2,4-oxadiazole moiety as potent histone deacetylase inhibitors. Eur J Med Chem 2015; 96:1-13. [DOI: 10.1016/j.ejmech.2015.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
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20
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Jiang T, Zhou Y, Zhu J, Chen Z, Sun P, Zhang Q, Wang Z, Shao Q, Jiang X, Li B, Wang H, Zhu W, Shen J. Design, synthesis, and pharmacological evaluation of highly potent and selective dipeptidyl peptidase-4 inhibitors. Arch Pharm (Weinheim) 2015; 348:399-407. [PMID: 25871012 DOI: 10.1002/ardp.201500082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/06/2015] [Indexed: 11/07/2022]
Abstract
The optimization of a series of fused β-homophenylalanine inhibitors of dipeptidyl peptidase-4 (DPP-4) is described. Modification on the P2-binding moiety of 6 (IC50 = 10 nM) led to the discovery of β-homophenylalanine derivatives containing pyrrolidin-2-ylmethyl amides. The introduction of a sulfamine in the meta position of the phenyl ring improved the potency against DPP-4 (6-12-fold increase). Compound 14k showed DPP-4 inhibitory activity with an IC50 value of 0.87 nM. Meanwhile, in vivo experiments exhibited that 14h had an efficiency comparable to sitagliptin at the dose of 10 mg/kg.
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Affiliation(s)
- Tao Jiang
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuren Zhou
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianming Zhu
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhuxi Chen
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Peng Sun
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhang
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhen Wang
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Shao
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiangrui Jiang
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bo Li
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Heyao Wang
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jingshan Shen
- Drug Discovery and Design Center, Key Laboratory for Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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21
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Parenti MD, Bruzzone S, Nencioni A, Del Rio A. Selectivity hot-spots of sirtuin catalytic cores. MOLECULAR BIOSYSTEMS 2015; 11:2263-72. [DOI: 10.1039/c5mb00205b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report a comprehensive study aimed to classify and identify the selectivity hot-spots for targeting the catalytic cores of human sirtuins using small molecule modulators.
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Affiliation(s)
- Marco Daniele Parenti
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)
- University of Bologna
- 40126 Bologna
- Italy
| | - Santina Bruzzone
- Department of Experimental Medicine
- Section of Biochemistry
- and CEBR
- University of Genoa
- 16132 Genoa
| | - Alessio Nencioni
- Department of Internal Medicine
- University of Genoa
- 16132 Genoa
- Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)
- University of Bologna
- 40126 Bologna
- Italy
- Institute of Organic Synthesis and Photoreactivity (ISOF)
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22
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Di Fruscia P, Zacharioudakis E, Liu C, Moniot S, Laohasinnarong S, Khongkow M, Harrison IF, Koltsida K, Reynolds CR, Schmidtkunz K, Jung M, Chapman KL, Steegborn C, Dexter DT, Sternberg MJE, Lam EWF, Fuchter MJ. The discovery of a highly selective 5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-4(3H)-one SIRT2 inhibitor that is neuroprotective in an in vitro Parkinson's disease model. ChemMedChem 2014; 10:69-82. [PMID: 25395356 DOI: 10.1002/cmdc.201402431] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 02/03/2023]
Abstract
Sirtuins, NAD(+) -dependent histone deacetylases (HDACs), have recently emerged as potential therapeutic targets for the treatment of a variety of diseases. The discovery of potent and isoform-selective inhibitors of this enzyme family should provide chemical tools to help determine the roles of these targets and validate their therapeutic value. Herein, we report the discovery of a novel class of highly selective SIRT2 inhibitors, identified by pharmacophore screening. We report the identification and validation of 3-((2-methoxynaphthalen-1-yl)methyl)-7-((pyridin-3-ylmethyl)amino)-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-4(3H)-one (ICL-SIRT078), a substrate-competitive SIRT2 inhibitor with a Ki value of 0.62 ± 0.15 μM and more than 50-fold selectivity against SIRT1, 3 and 5. Treatment of MCF-7 breast cancer cells with ICL-SIRT078 results in hyperacetylation of α-tubulin, an established SIRT2 biomarker, at doses comparable with the biochemical IC50 data, while suppressing MCF-7 proliferation at higher concentrations. In concordance with the recent reports that suggest SIRT2 inhibition is a potential strategy for the treatment of Parkinson's disease, we find that compound ICL-SIRT078 has a significant neuroprotective effect in a lactacystin-induced model of Parkinsonian neuronal cell death in the N27 cell line. These results encourage further investigation into the effects of ICL-SIRT078, or an optimised derivative thereof, as a candidate neuroprotective agent in in vivo models of Parkinson's disease.
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Affiliation(s)
- Paolo Di Fruscia
- Department of Chemistry, Imperial College London, St. Kensington Campus, London SW7 2AZ, (UK)
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23
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Cui H, Kamal Z, Ai T, Xu Y, More SS, Wilson DJ, Chen L. Discovery of potent and selective sirtuin 2 (SIRT2) inhibitors using a fragment-based approach. J Med Chem 2014; 57:8340-57. [PMID: 25275824 DOI: 10.1021/jm500777s] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sirtuin 2 (SIRT2) is one of the sirtuins, a family of NAD(+)-dependent deacetylases that act on a variety of histone and non-histone substrates. Accumulating biological functions and potential therapeutic applications have drawn interest in the discovery and development of SIRT2 inhibitors. Herein we report our discovery of novel SIRT2 inhibitors using a fragment-based approach. Inspired by the purported close binding proximity of suramin and nicotinamide, we prepared two sets of fragments, namely, the naphthylamide sulfonic acids and the naphthalene-benzamides and -nicotinamides. Biochemical evaluation of these two series provided structure-activity relationship (SAR) information, which led to the design of (5-benzamidonaphthalen-1/2-yloxy)nicotinamide derivatives. Among these inhibitors, one compound exhibited high anti-SIRT2 activity (48 nM) and excellent selectivity for SIRT2 over SIRT1 and SIRT3. In vitro, it also increased the acetylation level of α-tubulin, a well-established SIRT2 substrate, in both concentration- and time-dependent manners. Further kinetic studies revealed that this compound behaves as a competitive inhibitor against the peptide substrate and most likely as a noncompetitive inhibitor against NAD(+). Taken together, these results indicate that we have discovered a potent and selective SIRT2 inhibitor whose novel structure merits further exploration.
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Affiliation(s)
- Huaqing Cui
- Center for Drug Design, Academic Health Center, University of Minnesota , 516 Delaware Street SE, Minneapolis, Minnesota 55455, United States
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