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Bhandari N, Pfeiffer SC, Jaramillo-Lambert A. Characterization of N- and C-terminal endogenously tagged Tyrosyl-DNA phosphodiesterase 2 (TDPT-1) C. elegans strains. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000540. [PMID: 35622466 PMCID: PMC9010224 DOI: 10.17912/micropub.biology.000540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/09/2022]
Abstract
We have generated Tyrosyl-DNA phosphodiesterase 2 (TDPT-1) C. elegans strains where CRISPR/Cas9 was used to endogenously tag the protein at either the C- or N-terminus and validated the functionality of the resulting tagged TDPT-1 proteins. We have found that both the N-terminally tagged ( wrmScarlet::tdpt-1) and C-terminally tagged ( tdpt-1::3xflag ) worm TDPT-1 does not affect embryonic viability compared to wild type. Using the N-terminally tagged wrmScarlet::tdpt-1 strain we show, for the first time, that TDPT-1 is expressed in nuclei of the germ line and the soma. Moreover, we validate the expression of TDPT-1 at the protein level using the C-terminally tagged ( tdpt-1::3xflag ) strain.
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2
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Crewe M, Madabhushi R. Topoisomerase-Mediated DNA Damage in Neurological Disorders. Front Aging Neurosci 2021; 13:751742. [PMID: 34899270 PMCID: PMC8656403 DOI: 10.3389/fnagi.2021.751742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022] Open
Abstract
The nervous system is vulnerable to genomic instability and mutations in DNA damage response factors lead to numerous developmental and progressive neurological disorders. Despite this, the sources and mechanisms of DNA damage that are most relevant to the development of neuronal dysfunction are poorly understood. The identification of primarily neurological abnormalities in patients with mutations in TDP1 and TDP2 suggest that topoisomerase-mediated DNA damage could be an important underlying source of neuronal dysfunction. Here we review the potential sources of topoisomerase-induced DNA damage in neurons, describe the cellular mechanisms that have evolved to repair such damage, and discuss the importance of these repair mechanisms for preventing neurological disorders.
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3
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Swan RL, Cowell IG, Austin CA. Mechanisms to repair stalled Topoisomerase II-DNA covalent complexes. Mol Pharmacol 2021; 101:24-32. [PMID: 34689119 DOI: 10.1124/molpharm.121.000374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
DNA topoisomerases regulate the topological state of DNA, relaxing DNA supercoils and resolving catenanes and knots that result from biological processes such as transcription and replication. DNA topoisomerase II (TOP2) enzymes achieve this by binding DNA and introducing an enzyme-bridged DNA double-strand break (DSB) where each protomer of the dimeric enzyme is covalently attached to the 5' end of the cleaved DNA via an active site tyrosine phosphodiester linkage. The enzyme then passes a second DNA duplex though the DNA break, before religation and release of the enzyme. However, this activity is potentially hazardous to the cell, as failure to complete religation leads to persistent TOP2 protein-DNA covalent complexes which are cytotoxic. Indeed, this property of topoisomerase has been exploited in cancer therapy in the form of topoisomerase poisons which block the religation stage of the reaction cycle, leading to an accumulation of topoisomerase-DNA adducts. A number of parallel cellular processes have been identified that lead to removal of these covalent TOP2-DNA complexes facilitating repair of the resulting protein-free DSB by standard DNA repair pathways. These pathways presumably arose to repair spontaneous stalled or poisoned TOP2-DNA complexes, but understanding their mechanisms also has implications for cancer therapy, particularly resistance to anti-cancer TOP2 poisons and the genotoxic side effects of these drugs. Here we review recent progress in the understanding of the processing to TOP2 DNA covalent complexes., The basic components and mechanisms plus the additional layer of complexity posed by the post-translational modifications that modulate these pathways. Significance Statement Multiple pathways have been reported for removal and repair of TOP2-DNA covalent complexes to ensure the timely and efficient repair of TOP2-DNA covalent adducts to protect the genome. Post-translational modifications such as ubiquitination and SUMOylation are involved in the regulation of TOP2-DNA complex repair. Small molecule inhibitors of these post translational modifications may help to improve outcomes of TOP2 poison chemotherapy, for example by increasing TOP2 poison cytotoxicity and reducing genotoxicity, but this remains to be determined.
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Affiliation(s)
- Rebecca L Swan
- Biosciences Institute, Newcastle University, United Kingdom
| | - Ian G Cowell
- Institute for Cell and Molecular Biosciences, Newcastle University, United Kingdom
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4
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Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA, Cortés-Ledesma F, Williams RS. Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2. Nucleic Acids Res 2020; 48:6310-6325. [PMID: 32356875 DOI: 10.1093/nar/gkaa318] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/30/2020] [Accepted: 04/20/2020] [Indexed: 11/12/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) reverses Topoisomerase 2 DNA-protein crosslinks (TOP2-DPCs) in a direct-reversal pathway licensed by ZATTZNF451 SUMO2 E3 ligase and SUMOylation of TOP2. TDP2 also binds ubiquitin (Ub), but how Ub regulates TDP2 functions is unknown. Here, we show that TDP2 co-purifies with K63 and K27 poly-Ubiquitinated cellular proteins independently of, and separately from SUMOylated TOP2 complexes. Poly-ubiquitin chains of ≥ Ub3 stimulate TDP2 catalytic activity in nuclear extracts and enhance TDP2 binding of DNA-protein crosslinks in vitro. X-ray crystal structures and small-angle X-ray scattering analysis of TDP2-Ub complexes reveal that the TDP2 UBA domain binds K63-Ub3 in a 1:1 stoichiometric complex that relieves a UBA-regulated autoinhibitory state of TDP2. Our data indicates that that poly-Ub regulates TDP2-catalyzed TOP2-DPC removal, and TDP2 single nucleotide polymorphisms can disrupt the TDP2-Ubiquitin interface.
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Affiliation(s)
- Matthew J Schellenberg
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - C Denise Appel
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Amanda A Riccio
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Logan R Butler
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jenna A Liebermann
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide-Junta de Andalucía, 41092 Sevilla, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide-Junta de Andalucía, 41092 Sevilla, Spain.,Topology and DNA breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | - R Scott Williams
- Structural Cell Biology Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, US Department of Health and Human Services, Research Triangle Park, NC 27709, USA
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5
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Ambrose RL, Brice AM, Caputo AT, Alexander MR, Tribolet L, Liu YC, Adams TE, Bean AG, Stewart CR. Molecular characterisation of ILRUN, a novel inhibitor of proinflammatory and antimicrobial cytokines. Heliyon 2020; 6:e04115. [PMID: 32518853 PMCID: PMC7270589 DOI: 10.1016/j.heliyon.2020.e04115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/28/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
Regulation of type-I interferon (IFN) production is essential to the balance between antimicrobial defence and autoimmune disorders. The human protein-coding gene ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains, previously C6orf106) was recently characterised as an inhibitor of antiviral and proinflammatory cytokine (interferon-alpha/beta and tumor necrosis factor alpha) transcription. Currently there is a paucity of information about the molecular characteristics of ILRUN, despite it being associated with several diseases including virus infection, coronary artery disease, obesity and cancer. Here, we characterise ILRUN as a highly phylogenetically conserved protein containing UBA-like and a NBR1-like domains that are both essential for inhibition of type-I interferon and tumor necrosis factor alpha) transcription in human cells. We also solved the crystal structure of the NBR1-like domain, providing insights into its potential role in ILRUN function. This study provides critical information for future investigations into the role of ILRUN in health and disease.
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Affiliation(s)
- Rebecca L. Ambrose
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Aaron M. Brice
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | | | - Marina R. Alexander
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Leon Tribolet
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Yu Chih Liu
- CSIRO Manufacturing, Parkville, Victoria, 3010, Australia
| | | | - Andrew G.D. Bean
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
| | - Cameron R. Stewart
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, 3220, Australia
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6
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Sun Y, Saha S, Wang W, Saha LK, Huang SYN, Pommier Y. Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC). DNA Repair (Amst) 2020; 89:102837. [PMID: 32200233 DOI: 10.1016/j.dnarep.2020.102837] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022]
Abstract
Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots and catenanes that arise from replication, transcription, chromatin remodeling and other nucleic acid metabolic processes. They are also the targets of widely used anticancer drugs (e.g. topotecan, irinotecan, enhertu, etoposide, doxorubicin, mitoxantrone) and fluoroquinolone antibiotics (e.g. ciprofloxacin and levofloxacin). Topoisomerases manipulate DNA topology by cleaving one DNA strand (TOP1 and TOP3 enzymes) or both in concert (TOP2 enzymes) through the formation of transient enzyme-DNA cleavage complexes (TOPcc) with phosphotyrosyl linkages between DNA ends and the catalytic tyrosyl residue of the enzymes. Failure in the self-resealing of TOPcc results in persistent TOPcc (which we refer it to as topoisomerase DNA-protein crosslinks (TOP-DPC)) that threaten genome integrity and lead to cancers and neurodegenerative diseases. The cell prevents the accumulation of topoisomerase-mediated DNA damage by excising TOP-DPC and ligating the associated breaks using multiple pathways conserved in eukaryotes. Tyrosyl-DNA phosphodiesterases (TDP1 and TDP2) cleave the tyrosyl-DNA bonds whereas structure-specific endonucleases such as Mre11 and XPF (Rad1) incise the DNA phosphodiester backbone to remove the TOP-DPC along with the adjacent DNA segment. The proteasome and metalloproteases of the WSS1/Spartan family typify proteolytic repair pathways that debulk TOP-DPC to make the peptide-DNA bonds accessible to the TDPs and endonucleases. The purpose of this review is to summarize our current understanding of how the cell excises TOP-DPC and why, when and where the cell recruits one specific mechanism for repairing topoisomerase-mediated DNA damage, acquiring resistance to therapeutic topoisomerase inhibitors and avoiding genomic instability, cancers and neurodegenerative diseases.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sourav Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wenjie Wang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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7
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Riccio AA, Schellenberg MJ, Williams RS. Molecular mechanisms of topoisomerase 2 DNA-protein crosslink resolution. Cell Mol Life Sci 2020; 77:81-91. [PMID: 31728578 PMCID: PMC6960353 DOI: 10.1007/s00018-019-03367-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
The compaction of DNA and the continuous action of DNA transactions, including transcription and DNA replication, create complex DNA topologies that require Type IIA Topoisomerases, which resolve DNA topological strain and control genome dynamics. The human TOP2 enzymes catalyze their reactions via formation of a reversible covalent enzyme DNA-protein crosslink, the TOP2 cleavage complex (TOP2cc). Spurious interactions of TOP2 with DNA damage, environmental toxicants and chemotherapeutic "poisons" perturbs the TOP2 reaction cycle, leading to an accumulation of DNA-protein crosslinks, and ultimately, genomic instability and cell death. Emerging evidence shows that TOP2-DNA protein crosslink (DPC) repair entails multiple strand break repair activities, such as removal of the poisoned TOP2 protein and rejoining of the DNA ends through homologous recombination (HR) or non-homologous end joining (NHEJ). Herein, we discuss the molecular mechanisms of TOP2-DPC resolution, with specific emphasis on the recently uncovered ZATTZnf451-licensed TDP2-catalyzed TOP2-DPC reversal mechanism.
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Affiliation(s)
- Amanda A Riccio
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - Matthew J Schellenberg
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA
| | - R Scott Williams
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA.
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8
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Kawale AS, Povirk LF. Tyrosyl-DNA phosphodiesterases: rescuing the genome from the risks of relaxation. Nucleic Acids Res 2019; 46:520-537. [PMID: 29216365 PMCID: PMC5778467 DOI: 10.1093/nar/gkx1219] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022] Open
Abstract
Tyrosyl–DNA Phosphodiesterases 1 (TDP1) and 2 (TDP2) are eukaryotic enzymes that clean-up after aberrant topoisomerase activity. While TDP1 hydrolyzes phosphotyrosyl peptides emanating from trapped topoisomerase I (Top I) from the 3′ DNA ends, topoisomerase 2 (Top II)-induced 5′-phosphotyrosyl residues are processed by TDP2. Even though the canonical functions of TDP1 and TDP2 are complementary, they exhibit little structural or sequence similarity. Homozygous mutations in genes encoding these enzymes lead to the development of severe neurodegenerative conditions due to the accumulation of transcription-dependent topoisomerase cleavage complexes underscoring the biological significance of these enzymes in the repair of topoisomerase–DNA lesions in the nervous system. TDP1 can promiscuously process several blocked 3′ ends generated by DNA damaging agents and nucleoside analogs in addition to hydrolyzing 3′-phosphotyrosyl residues. In addition, deficiency of these enzymes causes hypersensitivity to anti-tumor topoisomerase poisons. Thus, TDP1 and TDP2 are promising therapeutic targets and their inhibitors are expected to significantly synergize the effects of current anti-tumor therapies including topoisomerase poisons and other DNA damaging agents. This review covers the structural aspects, biology and regulation of these enzymes, along with ongoing developments in the process of discovering safe and effective TDP inhibitors.
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Affiliation(s)
- Ajinkya S Kawale
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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9
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Chou AC, Aslanian A, Sun H, Hunter T. An internal ribosome entry site in the coding region of tyrosyl-DNA phosphodiesterase 2 drives alternative translation start. J Biol Chem 2018; 294:2665-2677. [PMID: 30593505 DOI: 10.1074/jbc.ra118.006269] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/26/2018] [Indexed: 11/06/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a multifunctional protein that has been implicated in a myriad of cellular pathways. Although most well-known for its phosphodiesterase activity removing stalled topoisomerase 2 from DNA, TDP2 has also been shown to interact with both survival and apoptotic mitogen-activated protein kinase (MAPK) signaling cascades. Moreover, it facilitates enterovirus replication and has been genetically linked to neurological disorders ranging from Parkinson's disease to dyslexia. To accurately evaluate TDP2 as a therapeutic target, we need to understand how TDP2 performs such a wide diversity of functions. Here, we use cancer cell lines modified with CRISPR/Cas9 or stably-expressed TDP2-targeted shRNA and transfection of various TDP2 mutants to show that its expression is regulated at the translational level via an internal ribosome entry site (IRES) that initiates translation at codon 54, the second in-frame methionine of the TDP2 coding sequence. We observed that this IRES drives expression of a shorter, N-terminally truncated isoform of TDP2, ΔN-TDP2, which omits a nuclear localization sequence. Additionally, we noted that ΔN-TDP2 retains phosphodiesterase activity and is protective against etoposide-induced cell death, but co-immunoprecipitates with fewer high-molecular-weight ubiquitinated peptide species, suggesting partial loss-of-function of TDP2's ubiquitin-association domain. In summary, our findings suggest the existence of an IRES in the 5' coding sequence of TDP2 that translationally regulates expression of an N-terminally truncated, cytoplasmic isoform of TDP2. These results shed light on the regulation of this multifunctional protein and may inform the design of therapies targeting TDP2 and associated pathways.
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Affiliation(s)
- Annie C Chou
- From the Graduate Program in Biomedical Sciences, University of California, San Diego, La Jolla, California 92093 and.,the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Aaron Aslanian
- the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Huaiyu Sun
- the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Tony Hunter
- the Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
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10
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Yu LM, Hu Z, Chen Y, Ravji A, Lopez S, Plescia CB, Yu Q, Yang H, Abdelmalak M, Saha S, Agama K, Kiselev E, Marchand C, Pommier Y, An LK. Synthesis and structure-activity relationship of furoquinolinediones as inhibitors of Tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Med Chem 2018; 151:777-796. [PMID: 29677635 DOI: 10.1016/j.ejmech.2018.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a recently discovered enzyme specifically repairing topoisomerase II (TOP2)-mediated DNA damage. It has been shown that inhibition of TDP2 synergize with TOP2 inhibitors. Herein, we report the discovery of the furoquinolinedione chemotype as a suitable skeleton for the development of selective TDP2 inhibitors. Compound 1 was identified as a TDP2 inhibitor as a result of screening our in-house compound library for compounds selective for TDP2 vs. TDP1. Further SAR studies provide several selective TDP2 inhibitors at low-micromolar range. The most potent compound 74 shows inhibitory activity with IC50 of 1.9 and 2.1 μM against recombinant TDP2 and TDP2 in whole cell extracts (WCE), respectively.
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Affiliation(s)
- Le-Mao Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhu Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Azhar Ravji
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Sophia Lopez
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Caroline B Plescia
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hui Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Monica Abdelmalak
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Sourav Saha
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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11
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New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Pharm Sci 2018; 118:67-79. [PMID: 29574079 DOI: 10.1016/j.ejps.2018.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 01/03/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase II (TOP2) mediated DNA damages and causes resistance to TOP2-targeted cancer therapy. Inhibiting TDP2 could sensitize cancer cells toward TOP2 inhibitors. However, potent TDP2 inhibitors with favorable physicochemical properties are not yet reported. Therefore, there is a need to search for novel molecular scaffolds capable of inhibiting TDP2. We report herein a new simple, robust, homogenous mix-and-read fluorescence biochemical assay based using humanized zebrafish TDP2 (14M_zTDP2), which provides biochemical and molecular structure basis for TDP2 inhibitor discovery. The assay was validated by screening a preselected library of 1600 compounds (Z' ≥ 0.72) in a 384-well format, and by running in parallel gel-based assays with fluorescent DNA substrates. This library was curated via virtual high throughput screening (vHTS) of 460,000 compounds from Chembridge Library, using the crystal structure of the novel surrogate protein 14M_zTDP2. From this primary screening, we selected the best 32 compounds (2% of the library) to further assess their TDP2 inhibition potential, leading to the IC50 determination of 10 compounds. Based on the dose-response curve profile, pan-assay interference compounds (PAINS) structure identification, physicochemical properties and efficiency parameters, two hit compounds, 11a and 19a, were tested using a novel secondary fluorescence gel-based assay. Preliminary structure-activity relationship (SAR) studies identified guanidine derivative 12a as an improved hit with a 6.4-fold increase in potency over the original HTS hit 11a. This study highlights the importance of the development of combination approaches (biochemistry, crystallography and high throughput screening) for the discovery of TDP2 inhibitors.
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12
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Huang SYN, Dalla Rosa I, Michaels SA, Tulumello DV, Agama K, Khiati S, Jean SR, Baechler SA, Factor VM, Varma S, Murai J, Miller Jenkins LM, Kelley SO, Pommier Y. Mitochondrial tyrosyl-DNA phosphodiesterase 2 and its TDP2 S short isoform. EMBO Rep 2018; 19:embr.201642139. [PMID: 29438979 DOI: 10.15252/embr.201642139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 12/04/2017] [Accepted: 01/05/2018] [Indexed: 12/26/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs abortive topoisomerase II cleavage complexes. Here, we identify a novel short isoform of TDP2 (TDP2S) expressed from an alternative transcription start site. TDP2S contains a mitochondrial targeting sequence, contributing to its enrichment in the mitochondria and cytosol, while full-length TDP2 contains a nuclear localization signal and the ubiquitin-associated domain in the N-terminus. Our study reveals that both TDP2 isoforms are present and active in the mitochondria. Comparison of isogenic wild-type (WT) and TDP2 knockout (TDP2-/-/-) DT40 cells shows that TDP2-/-/- cells are hypersensitive to mitochondrial-targeted doxorubicin (mtDox), and that complementing TDP2-/-/- cells with human TDP2 restores resistance to mtDox. Furthermore, mtDox selectively depletes mitochondrial DNA in TDP2-/-/- cells. Using CRISPR-engineered human cells expressing only the TDP2S isoform, we show that TDP2S also protects human cells against mtDox. Finally, lack of TDP2 in the mitochondria reduces the mitochondria transcription levels in two different human cell lines. In addition to identifying a novel TDP2S isoform, our report demonstrates the presence and importance of both TDP2 isoforms in the mitochondria.
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Affiliation(s)
- Shar-Yin N Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ilaria Dalla Rosa
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stephanie A Michaels
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - David V Tulumello
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Salim Khiati
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sae Rin Jean
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Simone A Baechler
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Valentina M Factor
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sudhir Varma
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Junko Murai
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Shana O Kelley
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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13
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Abstract
Recently, ZATT (also known as ZNF451 or Zpf451) was reported by Schellenberg et al. to aid the removal of Topoisomerase II cleavage complexes by stimulating the phosphodiesterase activity of Tyrosyl DNA Phosphodiesterase 2. Although the full implication of this discovery is unknown, it will help us understand how cells respond to topoisomerase-induced genome damage and chemotherapeutic topoisomerase 'poisons'.
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14
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Abstract
Covalent DNA-protein crosslinks (DPCs, also known as protein adducts) of topoisomerases and other proteins with DNA are highly toxic DNA lesions. Of note, chemical agents that induce DPCs include widely used classes of chemotherapeutics. Their bulkiness blocks virtually every chromatin-based process and makes them intractable for repair by canonical repair pathways. Distinct DPC repair pathways employ unique points of attack and are crucial for the maintenance of genome stability. Tyrosyl-DNA phosphodiesterases (TDPs) directly hydrolyse the covalent linkage between protein and DNA. The MRE11-RAD50-NBS1 (MRN) nuclease complex targets the DNA component of DPCs, excising the fragment affected by the lesion, whereas proteases of the spartan (SPRTN)/weak suppressor of SMT3 protein 1 (Wss1) family target the protein component. Loss of these pathways renders cells sensitive to DPC-inducing chemotherapeutics, and DPC repair pathways are thus attractive targets for combination cancer therapy.
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Affiliation(s)
- Julian Stingele
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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