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Yang J, Cassel J, Boyle BC, Oppong D, Ahn YH, Weiser BP. A homogeneous time-resolved fluorescence screen to identify SIRT2 deacetylase and defatty-acylase inhibitors. PLoS One 2024; 19:e0305000. [PMID: 38913635 PMCID: PMC11195995 DOI: 10.1371/journal.pone.0305000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
Human sirtuin-2 (SIRT2) has emerged as an attractive drug target for a variety of diseases. The enzyme is a deacylase that can remove chemically different acyl modifications from protein lysine residues. Here, we developed a high-throughput screen based on a homogeneous time-resolved fluorescence (HTRF) binding assay to identify inhibitors of SIRT2's demyristoylase activity, which is uncommon among many ligands that only affect its deacetylase activity. From a test screen of 9600 compounds, we identified a small molecule that inhibited SIRT2's deacetylase activity (IC50 = 7 μM) as well as its demyristoylase activity (IC50 = 37 μM). The inhibitor was composed of two small fragments that independently inhibited SIRT2: a halogenated phenol fragment inhibited its deacetylase activity, and a tricyclic thiazolobenzimidazole fragment inhibited its demyristoylase activity. The high-throughput screen also detected multiple deacetylase-specific SIRT2 inhibitors.
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Affiliation(s)
- Jie Yang
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, New Jersey, United States of America
- Department of Molecular Biology, Rowan-Virtua School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, United States of America
| | - Joel Cassel
- Molecular Screening & Protein Expression Facility, Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Brian C. Boyle
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, New Jersey, United States of America
- Department of Molecular Biology, Rowan-Virtua School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, United States of America
- Department of Biomedical Engineering, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Glassboro, New Jersey, United States of America
| | - Daniel Oppong
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Young-Hoon Ahn
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Brian P. Weiser
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, New Jersey, United States of America
- Department of Molecular Biology, Rowan-Virtua School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, United States of America
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2
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Yang J, Nicely NI, Weiser BP. Effects of Dimerization on the Deacylase Activities of Human SIRT2. Biochemistry 2023; 62:3383-3395. [PMID: 37966275 PMCID: PMC10702427 DOI: 10.1021/acs.biochem.3c00381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/05/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
Abstract
Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that is impaired in its ability to dimerize, which was confirmed with chemical cross-linking and in cells with a split-GFP approach. In enzyme assays, the SIRT2(Q142A/E340A) mutant had normal defatty-acylase activity and impaired deacetylase activity compared with the wild-type protein. These results indicate that dimerization is essential for optimal SIRT2 function as a deacetylase. Moreover, we show that SIRT2 dimers can be dissociated by a deacetylase and defatty-acylase inhibitor, ascorbyl palmitate. Our finding that its oligomeric state can affect the acyl substrate selectivity of SIRT2 is a novel mode of activity regulation by the enzyme that can be altered genetically or pharmacologically.
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Affiliation(s)
- Jie Yang
- Department
of Molecular Biology, Rowan University School
of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Nathan I. Nicely
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Brian P. Weiser
- Department
of Molecular Biology, Rowan University School
of Osteopathic Medicine, Stratford, New Jersey 08084, United States
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3
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In silico drug discovery of SIRT2 inhibitors from natural source as anticancer agents. Sci Rep 2023; 13:2146. [PMID: 36750593 PMCID: PMC9905574 DOI: 10.1038/s41598-023-28226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Sirtuin 2 (SIRT2) is a member of the sirtuin protein family, which includes lysine deacylases that are NAD+-dependent and organize several biological processes. Different forms of cancer have been associated with dysregulation of SIRT2 activity. Hence, identifying potent inhibitors for SIRT2 has piqued considerable attention in the drug discovery community. In the current study, the Natural Products Atlas (NPAtlas) database was mined to hunt potential SIRT2 inhibitors utilizing in silico techniques. Initially, the performance of the employed docking protocol to anticipate ligand-SIRT2 binding mode was assessed according to the accessible experimental data. Based on the predicted docking scores, the most promising NPAtlas molecules were selected and submitted to molecular dynamics (MD) simulations, followed by binding energy computations. Based on the MM-GBSA binding energy estimations over a 200 ns MD course, three NPAtlas compounds, namely NPA009578, NPA006805, and NPA001884, were identified with better ΔGbinding towards SIRT2 protein than the native ligand (SirReal2) with values of - 59.9, - 57.4, - 53.5, and - 49.7 kcal/mol, respectively. On the basis of structural and energetic assessments, the identified NPAtlas compounds were confirmed to be steady over a 200 ns MD course. The drug-likeness and pharmacokinetic characteristics of the identified NPAtlas molecules were anticipated, and robust bioavailability was predicted. Conclusively, the current results propose potent inhibitors for SIRT2 deserving more in vitro/in vivo investigation.
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Lin H. Substrate-selective small-molecule modulators of enzymes: Mechanisms and opportunities. Curr Opin Chem Biol 2023; 72:102231. [PMID: 36455490 PMCID: PMC9870951 DOI: 10.1016/j.cbpa.2022.102231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 11/29/2022]
Abstract
Small-molecule inhibitors of enzymes are widely used tools in reverse chemical genetics to probe biology and explore therapeutic opportunities. They are often compared with genetic knockdown or knockout and are expected to produce phenotypes similar to the genetic perturbations. This review aims to highlight that small molecule inhibitors of enzymes and genetic perturbations may not necessarily produce the same phenotype due to the possibility of substrate-selective or substrate-dependent effects of the inhibitors. Examples of substrate-selective inhibitors and the mechanisms for the substrate-selective effects are discussed. Substrate-selective modulators of enzymes have distinct advantages and cannot be easily replaced with biologics. Thus, they present an exciting opportunity for chemical biologists and medicinal chemists.
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Affiliation(s)
- Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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5
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Greenwood SN, Belz RG, Weiser BP. A Conserved Mechanism for Hormesis in Molecular Systems. Dose Response 2022; 20:15593258221109335. [PMID: 35936511 PMCID: PMC9350523 DOI: 10.1177/15593258221109335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Hormesis refers to dose-response phenomena where low dose treatments elicit a
response that is opposite the response observed at higher doses. Hormetic
dose-response relationships have been observed throughout all of biology, but
the underlying determinants of many reported hormetic dose-responses have not
been identified. In this report, we describe a conserved mechanism for hormesis
on the molecular level where low dose treatments enhance a response that becomes
reduced at higher doses. The hormetic mechanism relies on the ability of protein
homo-multimers to simultaneously interact with a substrate and a competitor on
different subunits at low doses of competitor. In this case, hormesis can be
observed if simultaneous binding of substrate and competitor enhances a response
of the homo-multimer. We characterized this mechanism of hormesis in binding
experiments that analyzed the interaction of homotrimeric proliferating cell
nuclear antigen (PCNA) with uracil DNA glycosylase (UNG2) and a
fluorescein-labeled peptide. Additionally, the basic features of this molecular
mechanism appear to be conserved with at least two enzymes that are stimulated
by low doses of inhibitor: dimeric BRAF and octameric glutamine synthetase 2
(GS2). Identifying such molecular mechanisms of hormesis may help explain
specific hormetic responses of cells and organisms treated with exogenous
compounds.
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Affiliation(s)
- Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
| | - Regina G Belz
- University of Hohenheim, Hans-Ruthenberg Institute, Stuttgart, Germany
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
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Djokovic N, Ruzic D, Rahnasto-Rilla M, Srdic-Rajic T, Lahtela-Kakkonen M, Nikolic K. Expanding the Accessible Chemical Space of SIRT2 Inhibitors through Exploration of Binding Pocket Dynamics. J Chem Inf Model 2022; 62:2571-2585. [PMID: 35467856 DOI: 10.1021/acs.jcim.2c00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Considerations of binding pocket dynamics are one of the crucial aspects of the rational design of binders. Identification of alternative conformational states or cryptic subpockets could lead to the discovery of completely novel groups of the ligands. However, experimental characterization of pocket dynamics, besides being expensive, may not be able to elucidate all of the conformational states relevant for drug discovery projects. In this study, we propose the protocol for computational simulations of sirtuin 2 (SIRT2) binding pocket dynamics and its integration into the structure-based virtual screening (SBVS) pipeline. Initially, unbiased molecular dynamics simulations of SIRT2:inhibitor complexes were performed using optimized force field parameters of SIRT2 inhibitors. Time-lagged independent component analysis (tICA) was used to design pocket-related collective variables (CVs) for enhanced sampling of SIRT2 pocket dynamics. Metadynamics simulations in the tICA eigenvector space revealed alternative conformational states of the SIRT2 binding pocket and the existence of a cryptic subpocket. Newly identified SIRT2 conformational states outperformed experimentally resolved states in retrospective SBVS validation. After performing prospective SBVS, compounds from the under-represented portions of the SIRT2 inhibitor chemical space were selected for in vitro evaluation. Two compounds, NDJ18 and NDJ85, were identified as potent and selective SIRT2 inhibitors, which validated the in silico protocol and opened up the possibility for generalization and broadening of its application. The anticancer effects of the most potent compound NDJ18 were examined on the triple-negative breast cancer cell line. Results indicated that NDJ18 represents a promising structure suitable for further evaluation.
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Affiliation(s)
- Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
| | - Minna Rahnasto-Rilla
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70210 Kuopio, Finland
| | - Tatjana Srdic-Rajic
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | | | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia
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Hong JY, Cassel J, Yang J, Lin H, Weiser BP. High-Throughput Screening Identifies Ascorbyl Palmitate as a SIRT2 Deacetylase and Defatty-Acylase Inhibitor. ChemMedChem 2021; 16:3484-3494. [PMID: 34382754 DOI: 10.1002/cmdc.202100343] [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: 05/18/2021] [Revised: 07/14/2021] [Indexed: 11/10/2022]
Abstract
Small-molecule inhibitors of the human sirtuin SIRT2 are being developed because of their therapeutic potential in a variety of diseases. Here, we developed a high-throughput screen to identify novel SIRT2 inhibitors using a fluorescent SIRT2 probe, 1-aminoanthracene (AMA). AMA has high fluorescence when bound to SIRT2, and its fluorescence reduces >10-fold when it is displaced from SIRT2 by other ligands. We used this property of AMA to screen a library of known bioactive compounds for SIRT2 binding and discovered two known pharmaceutical compounds that bind SIRT2 with Kd values in the low μM range, ascorbyl palmitate and pictilisib. Both compounds inhibit the deacetylase and defatty-acylase activities of SIRT2. While pictilisib has selectivity for SIRT2, ascorbyl palmitate also inhibits the enzymatic activities of SIRT1 and SIRT6. Finally, we show that ascorbyl palmitate inhibits SIRT2 deacetylase and defatty-acylase activities in cells, and SIRT2 inhibition by ascorbyl palmitate contributes to the cytotoxicity of the compound. Our work discovered novel SIRT2 deacylase inhibitors and presents a screening approach that can be applied on a larger scale.
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Affiliation(s)
- Jun Young Hong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Joel Cassel
- Molecular Screening & Protein Expression Facility, Wistar Institute, Philadelphia, PA, 19104, USA
| | - Jie Yang
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
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