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Chang CWM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD. A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase. Commun Chem 2024; 7:45. [PMID: 38418525 PMCID: PMC10901890 DOI: 10.1038/s42004-024-01129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
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Affiliation(s)
- Chiung-Wen Mary Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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2
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Singh BN, Achary VMM, Venkatapuram AK, Parmar H, Karippadakam S, Sopory SK, Reddy MK. Expression and functional analysis of various structural domains of tobacco topoisomerase II: To understand the mechanistic insights of plant type II topoisomerases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:302-314. [PMID: 36442361 DOI: 10.1016/j.plaphy.2022.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
In contrast to bacterial, yeast and animal systems, topoisomerases (topo) from plants have not been well studied. In this report, we generated four truncated topoisomerase II (Topo II) cDNA fragments encoding different functional domains of Nicotiana tabacum topo II (NtTopoII). Each of these recombinant polypeptides was expressed alone or in combination in temperature-sensitive topoisomerase II yeast mutants. Recombinant NtTopoII with truncated polypeptides fails to target the yeast nuclei and does not rescue the temperature-sensitive phenotype. In contrast complementation was achieved with the full-length NtTopoII, which localized to the yeast nucleus. These observations suggested the presence of a potent nuclear localization signal (NLS) in the extreme C-terminal 314 amino acid residues of NtTopoII that functioned effectively in the heterologous yeast system. Biochemical characterization of purified recombinant full-length and the partial NtTopoII polypeptides revealed that the ATP-binding and hydrolysis region of NtTopoIIwas located at 413 amino acid N-terminal region and this ATPase domain is functional both when it is expressed as a separate polypeptide or as part of the holoenzyme. The present findings also revealed that all NtTopoII truncated polypeptides were detrimental for in vitro supercoiled DNA relaxation and/or DNA nicking and ligation activity. Further, we discuss the possible disruption of coordinated macromolecular interface movements and the dimer interactions in truncated NtTopoII that are required for functional topoisomerase activity.
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Affiliation(s)
- Badri Nath Singh
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India
| | - V Mohan Murali Achary
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India.
| | - Ajay Kumar Venkatapuram
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India
| | - Hemangini Parmar
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India
| | - Sangeetha Karippadakam
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India
| | - Sudhir Kumar Sopory
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India.
| | - Malireddy K Reddy
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, Delhi, India.
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3
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Elton TS, Hernandez VA, Carvajal-Moreno J, Wang X, Ipinmoroti D, Yalowich JC. Intronic Polyadenylation in Acquired Cancer Drug Resistance Circumvented by Utilizing CRISPR/Cas9 with Homology-Directed Repair: The Tale of Human DNA Topoisomerase IIα. Cancers (Basel) 2022; 14:cancers14133148. [PMID: 35804920 PMCID: PMC9265003 DOI: 10.3390/cancers14133148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA topoisomerase IIα (170 kDa, TOP2α/170) resolves nucleic acid topological entanglements by generating transient double-strand DNA breaks. TOP2α inhibitors/poisons stabilize TOP2α-DNA covalent complexes resulting in persistent DNA damage and are frequently utilized to treat a variety of cancers. Acquired resistance to these chemotherapeutic agents is often associated with decreased TOP2α/170 expression levels. Studies have demonstrated that a reduction in TOP2α/170 results from a type of alternative polyadenylation designated intronic polyadenylation (IPA). As a consequence of IPA, variant TOP2α mRNA transcripts have been characterized that have resulted in the translation of C-terminal truncated TOP2α isoforms with altered biological activities. In this paper, an example is discussed where circumvention of acquired TOP2α-mediated drug resistance was achieved by utilizing CRISPR/Cas9 specific gene editing of an exon/intron boundary through homology directed repair (HDR) to reduce TOP2α IPA. These results illustrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant IPA. Abstract Intronic polyadenylation (IPA) plays a critical role in malignant transformation, development, progression, and cancer chemoresistance by contributing to transcriptome/proteome alterations. DNA topoisomerase IIα (170 kDa, TOP2α/170) is an established clinical target for anticancer agents whose efficacy is compromised by drug resistance often associated with a reduction of nuclear TOP2α/170 levels. In leukemia cell lines with acquired resistance to TOP2α-targeted drugs and reduced TOP2α/170 expression, variant TOP2α mRNA transcripts have been reported due to IPA that resulted in the translation of C-terminal truncated isoforms with altered nuclear-cytoplasmic distribution or heterodimerization with wild-type TOP2α/170. This review provides an overview of the various mechanisms regulating pre-mRNA processing and alternative polyadenylation, as well as the utilization of CRISPR/Cas9 specific gene editing through homology directed repair (HDR) to decrease IPA when splice sites are intrinsically weak or potentially mutated. The specific case of TOP2α exon 19/intron 19 splice site editing is discussed in etoposide-resistant human leukemia K562 cells as a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. This example supports the importance of aberrant IPA in acquired drug resistance to TOP2α-targeted drugs. In addition, these results demonstrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant splicing/polyadenylation.
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Janežič M, Valjavec K, Loboda KB, Herlah B, Ogris I, Kozorog M, Podobnik M, Grdadolnik SG, Wolber G, Perdih A. Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα. Int J Mol Sci 2021; 22:ijms222413474. [PMID: 34948269 PMCID: PMC8703789 DOI: 10.3390/ijms222413474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.
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Affiliation(s)
- Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Katja Valjavec
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Barbara Herlah
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Iza Ogris
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Mirijam Kozorog
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Marjetka Podobnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Simona Golič Grdadolnik
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2-4, 14195 Berlin, Germany;
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia; (M.J.); (K.V.); (K.B.L.); (B.H.); (I.O.); (M.K.); (M.P.); (S.G.G.)
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
- Correspondence: ; Tel.: +386-1-4760-376
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5
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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6
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Elton TS, Ozer HG, Yalowich JC. Effects of DNA topoisomerase IIα splice variants on acquired drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:161-170. [PMID: 32566920 PMCID: PMC7304410 DOI: 10.20517/cdr.2019.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA topoisomerase IIα (170 kDa, TOP2α/170) induces transient DNA double-strand breaks in proliferating cells to resolve DNA topological entanglements during chromosome condensation, replication, and segregation. Therefore, TOP2α/170 is a prominent target for anticancer drugs whose clinical efficacy is often compromised due to chemoresistance. Although many resistance mechanisms have been defined, acquired resistance of human cancer cell lines to TOP2α interfacial inhibitors/poisons is frequently associated with a reduction of Top2α/170 expression levels. Recent studies by our laboratory, in conjunction with earlier findings by other investigators, support the hypothesis that a major mechanism of acquired resistance to TOP2α-targeted drugs is due to alternative RNA processing/splicing. Specifically, several TOP2α mRNA splice variants have been reported which retain introns and are translated into truncated TOP2α isoforms lacking nuclear localization sequences and subsequent dysregulated nuclear-cytoplasmic disposition. In addition, intron retention can lead to truncated isoforms that lack both nuclear localization sequences and the active site tyrosine (Tyr805) necessary for forming enzyme-DNA covalent complexes and inducing DNA damage in the presence of TOP2α-targeted drugs. Ultimately, these truncated TOP2α isoforms result in decreased drug activity against TOP2α in the nucleus and manifest drug resistance. Therefore, the complete characterization of the mechanism(s) regulating the alternative RNA processing of TOP2α pre-mRNA may result in new strategies to circumvent acquired drug resistance. Additionally, novel TOP2α splice variants and truncated TOP2α isoforms may be useful as biomarkers for drug resistance, prognosis, and/or direct future TOP2α-targeted therapies.
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Affiliation(s)
- Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Hatice Gulcin Ozer
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
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7
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Kanagasabai R, Karmahapatra S, Kientz CA, Yu Y, Hernandez VA, Kania EE, Yalowich JC, Elton TS. The Novel C-terminal Truncated 90-kDa Isoform of Topoisomerase II α (TOP2 α/90) Is a Determinant of Etoposide Resistance in K562 Leukemia Cells via Heterodimerization with the TOP2 α/170 Isoform. Mol Pharmacol 2018; 93:515-525. [PMID: 29514855 PMCID: PMC11033944 DOI: 10.1124/mol.117.111567] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/28/2018] [Indexed: 02/06/2023] Open
Abstract
DNA topoisomerase IIα (170 kDa, TOP2α/170) is essential in proliferating cells by resolving DNA topological entanglements during chromosome condensation, replication, and segregation. We previously characterized a C-terminally truncated isoform (TOP2α/90), detectable in human leukemia K562 cells but more abundantly expressed in a clonal subline, K/VP.5, with acquired resistance to the anticancer agent etoposide. TOP2α/90 (786 aa) is the translation product of a TOP2α mRNA that retains a processed intron 19. TOP2α/90 lacks the active-site tyrosine-805 required to generate double-strand DNA breaks as well as nuclear localization signals present in the TOP2α/170 isoform (1531 aa). Here, we found that TOP2α/90, like TOP2α/170, was detectable in the nucleus and cytoplasm of K562 and K/VP.5 cells. Coimmunoprecipitation of endogenous TOP2α/90 and TOP2α/170 demonstrated heterodimerization of these isoforms. Forced expression of TOP2α/90 in K562 cells suppressed, whereas siRNA-mediated knockdown of TOP2α/90 in K/VP.5 cells enhanced, etoposide-mediated DNA strand breaks compared with similarly treated cells transfected with empty vector or control siRNAs, respectively. In addition, forced expression of TOP2α/90 in K562 cells inhibited etoposide cytotoxicity assessed by clonogenic assays. qPCR and immunoassays demonstrated TOP2α/90 mRNA and protein expression in normal human tissues/cells and in leukemia cells from patients. Together, results strongly suggest that TOP2α/90 expression decreases drug-induced TOP2α-DNA covalent complexes and is a determinant of chemoresistance through a dominant-negative effect related to heterodimerization with TOP2α/170. Alternative processing of TOP2α pre-mRNA, and subsequent synthesis of TOP2α/90, may be an important mechanism regulating the formation and/or stability of cytotoxic TOP2α/170-DNA covalent complexes in response to TOP2α-targeting agents.
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MESH Headings
- Antineoplastic Agents, Alkylating/pharmacology
- Antineoplastic Agents, Alkylating/therapeutic use
- Cell Line
- Cell Nucleus/enzymology
- DNA Breaks, Double-Stranded/drug effects
- DNA Topoisomerases, Type II/chemistry
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- Dimerization
- Drug Resistance, Neoplasm
- Etoposide/pharmacology
- Etoposide/therapeutic use
- Humans
- Isoenzymes/chemistry
- Isoenzymes/genetics
- Isoenzymes/metabolism
- K562 Cells
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- RNA Processing, Post-Transcriptional
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Affiliation(s)
- Ragu Kanagasabai
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | | | - Corey A Kientz
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Yang Yu
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Victor A Hernandez
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Evan E Kania
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Jack C Yalowich
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Terry S Elton
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
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8
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Lee JH, Wendorff TJ, Berger JM. Resveratrol: A novel type of topoisomerase II inhibitor. J Biol Chem 2017; 292:21011-21022. [PMID: 29074616 DOI: 10.1074/jbc.m117.810580] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/18/2017] [Indexed: 02/04/2023] Open
Abstract
Resveratrol, a polyphenol found in various plant sources, has gained attention as a possible agent responsible for the purported health benefits of certain foods, such as red wine. Despite annual multi-million dollar market sales as a nutriceutical, there is little consensus about the physiological roles of resveratrol. One suggested molecular target of resveratrol is eukaryotic topoisomerase II (topo II), an enzyme essential for chromosome segregation and DNA supercoiling homeostasis. Interestingly, resveratrol is chemically similar to ICRF-187, a clinically approved chemotherapeutic that stabilizes an ATP-dependent dimerization interface in topo II to block enzyme activity. Based on this similarity, we hypothesized that resveratrol may antagonize topo II by a similar mechanism. Using a variety of biochemical assays, we find that resveratrol indeed acts through the ICRF-187 binding locus, but that it inhibits topo II by preventing ATPase domain dimerization rather than stabilizing it. This work presents the first comprehensive analysis of the biochemical effects of both ICRF-187 and resveratrol on the human isoforms of topo II, and reveals a new mode for the allosteric regulation of topo II through modulation of ATPase status. Natural polyphenols related to resveratrol that have been shown to impact topo II function may operate in a similar manner.
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Affiliation(s)
- Joyce H Lee
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | - Timothy J Wendorff
- the Biophysics Graduate Program, University of California, Berkeley, California 94720
| | - James M Berger
- From the Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
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9
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Andrei SA, Sijbesma E, Hann M, Davis J, O’Mahony G, Perry MWD, Karawajczyk A, Eickhoff J, Brunsveld L, Doveston RG, Milroy LG, Ottmann C. Stabilization of protein-protein interactions in drug discovery. Expert Opin Drug Discov 2017; 12:925-940. [DOI: 10.1080/17460441.2017.1346608] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sebastian A. Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Michael Hann
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, UK
| | - Gavin O’Mahony
- CVMD Medicinal Chemistry, Innovative Medicines and Early Development, AstraZeneca Gothenburg, Pepparedsleden, Mölndal, Sweden
| | - Matthew W. D. Perry
- RIA Medicinal Chemistry, Innovative Medicines and Early Development, AstraZeneca Gothenburg, Pepparedsleden, Mölndal, Sweden
| | - Anna Karawajczyk
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Dortmund, Germany
| | - Jan Eickhoff
- Assay development & screening, Lead Discovery Center GmbH, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Richard G. Doveston
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Essen, Germany
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10
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Huang WC, Lee CY, Hsieh TS. Single-molecule Förster resonance energy transfer (FRET) analysis discloses the dynamics of the DNA-topoisomerase II (Top2) interaction in the presence of TOP2-targeting agents. J Biol Chem 2017. [PMID: 28630044 DOI: 10.1074/jbc.m117.792861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerases play crucial roles in DNA replication, transcription, and recombination. For instance, topoisomerase II (Top2) is critically important for resolving DNA tangles during cell division, and as such, it is a broad anticancer drug target. Top2 regulates DNA topology by transiently breaking one double-stranded DNA molecule (cleavage), allowing a second double strand to pass through the opened DNA gate (opening), and then closing the gate by rejoining the broken ends. Drugs that modulate Top2 catalysis may therefore affect enzymatic activity at several different steps. Previous studies have focused on examining DNA cleavage and ligation; however, the dynamic opening and closing of the DNA gate has been less explored. Here, we used the single-molecule Förster resonance energy transfer (smFRET) method to observe the open and closed state of the DNA gate and to measure dwell times in each state. Our results show that Top2 binds and bends DNA to increase the energy transfer efficiency (EFRET), and ATP treatment further induces the fluctuation of EFRET, representing the gate opening and closing. Additionally, our results demonstrate that both types of Top2-targeting anticancer drugs, the catalytic inhibitor dexrazoxane (ICRF187) and mechanistic poison teniposide (VM26), can interfere with DNA gate dynamics and shorten the dwell time in the closed state. Moreover, Top2 bound to the nonhydrolyzable ATP analog 5'-adenylyl-β,γ-imidodiphosphate exhibits altered DNA gate dynamics, but the DNA gate appears to open and close even after N-gate closure. In summary, we have utilized single-molecule detection to unravel Top2 DNA gate dynamics and reveal previously unknown effects of Top2 drugs on these dynamics.
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Affiliation(s)
- Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Chun-Ying Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Tao-Shih Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; Department of Chemistry, National Taiwan University, Taipei 106, Taiwan; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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11
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Janežič M, Pogorelčnik B, Brvar M, Solmajer T, Perdih A. 3-substituted-1H-indazoles as Catalytic Inhibitors of the Human DNA Topoisomerase IIα. ChemistrySelect 2017. [DOI: 10.1002/slct.201601554] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matej Janežič
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | | | - Matjaž Brvar
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | - Tom Solmajer
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
| | - Andrej Perdih
- National Institute of Chemistry; Hajdrihova 19, SI- 1001 Ljubljana Slovenia
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12
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Kanagasabai R, Serdar L, Karmahapatra S, Kientz CA, Ellis J, Ritke MK, Elton TS, Yalowich JC. Alternative RNA Processing of Topoisomerase IIα in Etoposide-Resistant Human Leukemia K562 Cells: Intron Retention Results in a Novel C-Terminal Truncated 90-kDa Isoform. J Pharmacol Exp Ther 2016; 360:152-163. [PMID: 27974648 DOI: 10.1124/jpet.116.237107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/04/2016] [Indexed: 11/22/2022] Open
Abstract
DNA topoisomerase IIα (TOP2α) is a prominent target for anticancer drugs whose clinical efficacy is often limited by chemoresistance. Using antibody specific for the N-terminal of TOP2α, immunoassays indicated the existence of two TOP2α isoforms, 170 and 90 kDa, present in K562 leukemia cells and in an acquired etoposide (VP-16)-resistant clone (K/VP.5). TOP2α/90 expression was dramatically increased in etoposide-resistant K/VP.5 compared with parental K562 cells. We hypothesized that TOP2α/90 was the translation product of novel alternatively processed pre-mRNA, confirmed by 3'-rapid amplification of cDNA ends, polymerase chain reaction, and sequencing. TOP2α/90 mRNA includes retained intron 19, which harbors an in-frame stop codon, and two consensus poly(A) sites. The processed transcript is polyadenylated. TOP2α/90 mRNA encodes a 90,076-Da translation product missing the C-terminal 770 amino acids of TOP2α/170, replaced by 25 unique amino acids through translation of the exon 19/intron 19 read-through. Immunoassays, utilizing antisera raised against these unique amino acids, confirmed that TOP2α/90 is expressed in both cell types, with overexpression in K/VP.5 cells. Immunodetection of complex of enzyme-to-DNA and single-cell gel electrophoresis (Comet) assays demonstrated that K562 cells transfected with a TOP2α/90 expression plasmid exhibited reduced etoposide-mediated TOP2α-DNA covalent complexes and decreased etoposide-induced DNA damage, respectively, compared with similarly treated K562 cells transfected with empty vector. Because TOP2α/90 lacks the active site tyrosine (Tyr805) of full-length TOP2α, these results strongly suggest that TOP2α/90 exhibits dominant-negative properties. Further studies are underway to characterize the mechanism(s) by which TOP2α/90 plays a role in acquired resistance to etoposide and other TOP2α targeting agents.
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Affiliation(s)
- Ragu Kanagasabai
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Lucas Serdar
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Soumendrakrishna Karmahapatra
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Corey A Kientz
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Justin Ellis
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Mary K Ritke
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Terry S Elton
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
| | - Jack C Yalowich
- Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio (R.K., L.S., S.K., C.A.K., J.E., T.S.E., J.C.Y.); James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio (J.C.Y.); and Department of Biology, University of Indianapolis, Indianapolis, Indiana (M.K.R.)
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Pogorelčnik B, Janežič M, Sosič I, Gobec S, Solmajer T, Perdih A. 4,6-Substituted-1,3,5-triazin-2(1H)-ones as monocyclic catalytic inhibitors of human DNA topoisomerase IIα targeting the ATP binding site. Bioorg Med Chem 2015; 23:4218-4229. [PMID: 26183545 DOI: 10.1016/j.bmc.2015.06.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
Human DNA topoisomerase IIα (htIIα) is a validated target for the development of novel anticancer agents. Starting from our discovered 4-amino-1,3,5-triazine inhibitors of htIIα, we investigated a library of 2,4,6-trisubstituted-1,3,5-triazines for novel inhibitors that bind to the htIIα ATP binding site using a combination of structure-based and ligand-based pharmacophore models and molecular docking. 4,6-substituted-1,3,5-triazin-2(1H)-ones 8, 9 and 14 were identified as novel inhibitors with activity comparable to the established drug etoposide (1). Compound 8 inhibits the htIIα decatenation in a superior fashion to etoposide. Cleavage assays demonstrated that selected compounds 8 and 14 do not act as poisons and antagonize the poison effect of etoposide. Microscale thermophoresis (MST) confirmed binding of compound 8 to the htIIα ATPase domain and compound 14 effectively inhibits the htIIα mediated ATP hydrolysis. The molecular dynamics simulation study provides further insight into the molecular recognition. The 4,6-disubstituted-1,3,5-triazin-2(1H)-ones represent the first validated monocyclic class of catalytic inhibitors that bind to the to the htIIα ATPase domain.
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Affiliation(s)
| | - Matej Janežič
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tom Solmajer
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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14
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Design, synthesis and biological evaluation of novel 7-alkylamino substituted benzo[a]phenazin derivatives as dual topoisomerase I/II inhibitors. Eur J Med Chem 2015; 92:540-53. [DOI: 10.1016/j.ejmech.2015.01.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 01/10/2015] [Accepted: 01/11/2015] [Indexed: 11/22/2022]
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15
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Snyder RD, Holt PA, Maguire JM, Trent JO. Evidence for the contribution of non-covalent steroid interactions between DNA and topoisomerase in the genotoxicity of steroids. Drug Chem Toxicol 2014; 38:212-9. [PMID: 24975547 DOI: 10.3109/01480545.2014.928725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fifty two steroids and 9 Vitamin D analogs were docked into ten crystallographically-defined DNA dinucleotide sites and two human topoisomerase II ATP binding sites using two computational programs, Autodock and Surflex. It is shown that both steroids and Vitamin D analogs exhibit a propensity for non-covalent intercalative binding to DNA. A higher predicted binding affinity was found, however, for steroids and the ATP binding site of topoisomerase; in fact these drugs exhibited among the highest topo II binding observed in over 1370 docked drugs. These findings along with genotoxicity data from 26 additional steroids not subjected to docking analysis, support a mechanism wherein the long known, but poorly understood, clastogenicity of steroids may be attributable to inhibition of topoisomerase. A "proof of principle" experiment with dexamethasone demonstrated this to be the likely mechanism of clastogenicity of, at least, this steroid. The generality of this proposed mechanism of genotoxicity across the steroids and vitamin-D analogs is discussed.
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Affiliation(s)
- Ronald D Snyder
- RDS Consulting Services , 3335 Grand Falls Blvd, Maineville, OH , United States and
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16
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Zhuo ST, Li CY, Hu MH, Chen SB, Yao PF, Huang SL, Ou TM, Tan JH, An LK, Li D, Gu LQ, Huang ZS. Synthesis and biological evaluation of benzo[a]phenazine derivatives as a dual inhibitor of topoisomerase I and II. Org Biomol Chem 2014; 11:3989-4005. [PMID: 23657605 DOI: 10.1039/c3ob40325d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Topoisomerases (Topo I and Topo II) are very important players in DNA replication, repair, and transcription, and are a promising class of antitumor target. In present study, a series of benzo[a]phenazine derivatives with alkylamino side chains at C-5 were designed, synthesized, and their biological activities were evaluated. Most of derivatives showed good antiproliferative activity with a range of IC50 values of 1-10 μM on the four cancer cell lines HeLa, A549, MCF-7, and HL-60. Topoisomerase-mediated DNA relaxation assay results showed that derivatives could effectively inhibit the activity of both Topo I and Topo II, and the structure-activity relationship studies indicated the importance of introducing an alkylamino side chain. Further mechanism studies revealed that the compounds could stabilize the Topo I-DNA cleavage complexes and inhibit the ATPase activity of hTopo II, indicating that they are a rare class of dual topoisomerase inhibitors by acting as Topo I poisons and Topo II catalytic inhibitors. Moreover, flow cytometric analysis and caspase-3/7 activation assay showed that this class of compounds could induce apoptosis of HL-60 cells.
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Affiliation(s)
- Shi-Tian Zhuo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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17
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Synthesis and dissolution of hemicatenanes by type IA DNA topoisomerases. Proc Natl Acad Sci U S A 2013; 110:E3587-94. [PMID: 24003117 DOI: 10.1073/pnas.1304103110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type IA DNA topoisomerases work with a unique mechanism of strand passage through an enzyme-bridged, ssDNA gate, thus enabling them to carry out diverse reactions in processing structures important for replication, recombination, and repair. Here we report a unique reaction mediated by an archaeal type IA topoisomerase, the synthesis and dissolution of hemicatenanes. We cloned, purified, and characterized an unusual type IA enzyme from a hyperthermophilic archaeum, Nanoarchaeum equitans, which is split into two pieces. The recombinant heterodimeric enzyme has the expected activities in its preference of relaxing negatively supercoiled DNA. Its amino acid sequence and cleavage site sequence analysis suggest that it is topoisomerase III, and therefore we named it "NeqTop3." At high enzyme concentrations, NeqTop3 can generate high-molecular-weight DNA networks. Biochemical and electron microscopic data indicate that the DNA networks are connected through hemicatenane linkages. The hemicatenane formation likely is mediated by the single-strand passage through denatured bubbles in the substrate DNA under high temperature. NeqTop3 at lower concentrations can reverse hemicatenanes. A complex of human topoisomerase 3α, Bloom helicase, and RecQ-mediated genome instability protein 1 and 2 can partially disentangle the hemicatenane network. Both the formation and dissolution of hemicatenanes by type IA topoisomerases demonstrate that these enzymes have an important role in regulating intermediates from replication, recombination, and repair.
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18
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Boonyalai N, Sittikul P, Pradidphol N, Kongkathip N. Biophysical and molecular docking studies of naphthoquinone derivatives on the ATPase domain of human topoisomerase II. Biomed Pharmacother 2012; 67:122-8. [PMID: 23089478 DOI: 10.1016/j.biopha.2012.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 08/26/2012] [Indexed: 10/27/2022] Open
Abstract
Numerous naphthoquinone derivatives, such as rhinacanthins function as anticancer drugs, which target hTopoII. The structure of hTopoII contains both an ATPase domain and a DNA binding domain. Several drugs bind to either one or both of these domains, thus modifying the activity of hTopoII. The naphthoquinone esters and amides used in this study showed that their hTopoIIα inhibitory activity was inversely proportional to ATP concentration. In order to better characterize the inhibitory action of these compounds, sufficient quantities of soluble functional hTopoII-ATPase domain were required. Therefore, both the alpha and beta isoforms of the hTopoII-ATPase domain were over-expressed in Escherichia coli. The hTopoIIα-ATPase activity was reduced in the presence of naphthoquinone derivatives. Additionally, a molecular docking study revealed that the selected naphthoquinone ester and amide bind to the ATP-binding domain of hTopoIIα. Collectively, the results here provide for the first time a novel insight into the interaction between naphthoquinone esters and amides, and the ATP-binding domain of hTopoIIα. The further elucidation of the mechanism of action of the naphthoquinone esters and amides inhibitory activity is essential.
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Affiliation(s)
- Nonlawat Boonyalai
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50, Phahon Yothin road, Chatuchak, 10900 Bangkok, Thailand.
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19
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Chen YT, Collins TRL, Guan Z, Chen VB, Hsieh TS. Probing conformational changes in human DNA topoisomerase IIα by pulsed alkylation mass spectrometry. J Biol Chem 2012; 287:25660-8. [PMID: 22679013 DOI: 10.1074/jbc.m112.377606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type II topoisomerases are essential enzymes for solving DNA topological problems by passing one segment of DNA duplex through a transient double-strand break in a second segment. The reaction requires the enzyme to precisely control DNA cleavage and gate opening coupled with ATP hydrolysis. Using pulsed alkylation mass spectrometry, we were able to monitor the solvent accessibilities around 13 cysteines distributed throughout human topoisomerase IIα by measuring the thiol reactivities with monobromobimane. Most of the measured reactivities are in accordance with the predicted ones based on a homology structural model generated from available crystal structures. However, these results reveal new information for both the residues not covered in the structural model and potential differences between the modeled and solution holoenzyme structures. Furthermore, on the basis of the reactivity changes of several cysteines located at the N-gate and DNA gate, we could monitor the movement of topoisomerase II in the presence of cofactors and detect differences in the DNA gate between two closed clamp enzyme conformations locked by either 5'-adenylyl β,γ-imidodiphosphate or the anticancer drug ICRF-193.
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Affiliation(s)
- Yu-Tsung Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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20
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Gurbani D, Kukshal V, Laubenthal J, Kumar A, Pandey A, Tripathi S, Arora A, Jain SK, Ramachandran R, Anderson D, Dhawan A. Mechanism of inhibition of the ATPase domain of human topoisomerase IIα by 1,4-benzoquinone, 1,2-naphthoquinone, 1,4-naphthoquinone, and 9,10-phenanthroquinone. Toxicol Sci 2012; 126:372-90. [PMID: 22218491 DOI: 10.1093/toxsci/kfr345] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The inhibition of human topoisomerase IIα (Hu-TopoIIα), a major enzyme involved in maintaining DNA topology, repair, and chromosome condensation/decondensation results in loss of genomic integrity. In the present study, the inhibition of ATPase domain of Hu-TopoIIα as a possible mechanism of genotoxicity of 1,4-benzoquinone (BQ), hydroquinone (HQ), naphthoquinone (1,2-NQ and 1,4-NQ), and 9,10-phenanthroquinone (9,10-PQ) was investigated. In silico modeling predicted that 1,4-BQ, 1,2-NQ, 1,4-NQ, and 9,10-PQ could interact with Ser-148, Ser-149, Asn-150, and Asn-91 residues of the ATPase domain of Hu-TopoIIα. Biochemical inhibition assays with the purified ATPase domain of Hu-TopoIIα revealed that 1,4-BQ is the most potent inhibitor followed by 1,4-NQ > 1,2-NQ > 9,10-PQ > HQ. Ligand-binding studies using isothermal titration calorimetry revealed that 1,4-BQ, HQ, 1,4-NQ, 1,2-NQ, and 9,10-PQ enter into four sequentially binding site models inside the domain. 1,4-BQ exhibited the strongest binding, followed by 1,4-NQ > 1,2-NQ > 9,10-PQ > HQ, as revealed by their average K(d) values. The cellular fate of such inhibition was further evidenced by an increase in the number of Hu-TopoIIα-DNA cleavage complexes in the human lung epithelial cells (BEAS-2B) using trapped in agarose DNA immunostaining (TARDIS) assay, which utilizes antibody specific for Hu-TopoIIα. Furthermore, the increase in γ-H2A.X levels quantitated by flow cytometry and visualized by immunofluorescence microscopy illustrated that accumulation of DNA double-strand breaks inside the cells can be attributed to the inhibition of Hu-TopoIIα. These findings collectively suggest that 1,4-BQ, 1,2-NQ, 1,4-NQ, and 9,10-PQ inhibit the ATPase domain and potentially result in Hu-TopoIIα-mediated clastogenic and leukemogenic events.
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Affiliation(s)
- Deepak Gurbani
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India
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21
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Lin RK, Zhou N, Lyu YL, Tsai YC, Lu CH, Kerrigan J, Chen YT, Guan Z, Hsieh TS, Liu LF. Dietary isothiocyanate-induced apoptosis via thiol modification of DNA topoisomerase IIα. J Biol Chem 2011; 286:33591-600. [PMID: 21828038 DOI: 10.1074/jbc.m111.258137] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies in animal models have indicated that dietary isothiocyanates (ITCs) exhibit cancer preventive activities through carcinogen detoxification-dependent and -independent mechanisms. The carcinogen detoxification-independent mechanism of cancer prevention by ITCs has been attributed at least in part to their ability to induce apoptosis of transformed (initiated) cells (e.g. through suppression of IκB kinase and nuclear factor κB as well as other proposed mechanisms). In the current studies we show that ITC-induced apoptosis of oncogene-transformed cells involves thiol modification of DNA topoisomerase II (Top2) based on the following observations. 1) siRNA-mediated knockdown of Top2α in both SV40-transformed MEFs and Ras-transformed human mammary epithelial MCF-10A cells resulted in reduced ITC sensitivity. 2) ITCs, like some anticancer drugs and cancer-preventive dietary components, were shown to induce reversible Top2α cleavage complexes in vitro. 3) ITC-induced Top2α cleavage complexes were abolished by co-incubation with excess glutathione. In addition, proteomic analysis revealed that several cysteine residues on human Top2α were covalently modified by benzyl-ITC, suggesting that ITC-induced Top2α cleavage complexes may involve cysteine modification. Interestingly, consistent with the thiol modification mechanism for Top2α cleavage complex induction, the thiol-reactive selenocysteine, but not the non-thiol-reactive selenomethionine, was shown to induce Top2α cleavage complexes. In the aggregate, our results suggest that thiol modification of Top2α may contribute to apoptosis induction in transformed cells by ITCs.
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Affiliation(s)
- Ren-Kuo Lin
- Department of Pharmacology and the Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, New Jersey 08854, USA
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22
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Huang H, Chen Q, Ku X, Meng L, Lin L, Wang X, Zhu C, Wang Y, Chen Z, Li M, Jiang H, Chen K, Ding J, Liu H. A series of alpha-heterocyclic carboxaldehyde thiosemicarbazones inhibit topoisomerase IIalpha catalytic activity. J Med Chem 2010; 53:3048-64. [PMID: 20353152 DOI: 10.1021/jm9014394] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of novel thiosemicarbazone derivatives bearing condensed heterocyclic carboxaldehyde moieties were designed and synthesized. Among them, TSC24 exhibited broad antiproliferative activity in a panel of human tumor cells and suppressed tumor growth in mice. The mechanism research revealed that TSC24 was not only an iron chelator but also a topoisomerase IIalpha catalytic inhibitor. Its inhibition on topoisomerase IIalpha was due to direct interaction with the ATPase domain of topoisomerase IIalpha which led to the block of ATP hydrolysis. Molecular docking predicted that TSC24 might bind at the ATP binding site, which was confirmed by the competitive inhibition assay. These results about the mechanisms involved in the anticancer activities of thiosemicarbazones will aid in the rational design of novel topoisomerase II-targeted drugs and will provide insights into the discovery and development of novel cancer therapeutics based on the dual activity to chelate iron and to inhibit the catalytic activity of topoisomerase IIalpha.
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Affiliation(s)
- He Huang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China
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23
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Xie P. Dynamics of strand passage catalyzed by topoisomerase II. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1251-9. [PMID: 20127325 DOI: 10.1007/s00249-010-0578-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/17/2009] [Accepted: 01/13/2010] [Indexed: 11/25/2022]
Abstract
DNA topoisomerase II is a homodimeric molecular machine that uses ATP hydrolysis to untangle DNA by passing one double-stranded DNA duplex (T-segment) through another double-stranded duplex (G-segment). However, despite extensive studies, the dynamics of ATP-dependent T-transport is still not very clear. Here, based on the proposal that transport of the T-segment through the transiently cleaved G-segment and the opened C-gate of the enzyme is via a free diffusion mechanism, the dynamics of T-transport are studied theoretically. Our results show that, to complete passage of the strand with nearly 100% efficiency, the C-gate is required to open by a width that is only slightly larger than the width of DNA duplex and for a time shorter than 100 micros in the presence of several k (B) T binding affinities of the T-segment for the B' domains. The results are implied by our understanding of the opening and closing dynamics of the C-gate. Moreover, the dependence of chemomechanical coupling efficiency on degrees of DNA supercoiling by gyrases can also be explained by using our results. On the basis of these theoretical results and previous experimental data, a modified two-gate model for chemomechanical coupling of the topoisomerase II enzyme is proposed.
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Affiliation(s)
- Ping Xie
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China.
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24
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Monitoring the topoisomerase II DNA gate conformational change with fluorescence resonance energy transfer. Methods Mol Biol 2009. [PMID: 19763942 DOI: 10.1007/978-1-60761-340-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Type II DNA topoisomerases are essential, ubiquitous enzymes responsible for performing vital functions in chromosome condensation and segregation and in regulating intracellular DNA supercoiling. Topoisomerase II (topo II) performs these DNA transactions by passing one segment of DNA through the other using a reversible, enzyme-bridged double-stranded DNA break. This cleavage/religation of the DNA backbone is coupled to the opening and closing of the DNA gate, a critical step for strand passage during the catalytic cycle. To monitor the opening and closing of the DNA gate, we designed an oligonucleotide substrate with a pair of fluorophores flanking the topoisomerase II cleavage site, such that the fluorophores undergo efficient fluorescence resonance energy transfer (FRET) in the intact DNA substrate, but the FRET efficiency decreases as topo II opens the DNA gate. Here we present a method for creating the DNA substrate and using it as a tool to monitor the conformational changes at the topo II DNA gate. We detail how to collect and process fluorescence spectra to determine the FRET efficiency of the DNA substrate.
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25
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A unique 45-amino-acid region in the toprim domain of Plasmodium falciparum gyrase B is essential for its activity. EUKARYOTIC CELL 2009; 8:1759-69. [PMID: 19700639 DOI: 10.1128/ec.00149-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA gyrase is the only topoisomerase that can introduce negative supercoils into the DNA at the cost of ATP hydrolysis. Some but not all the steps of the topoisomerization reaction are understood clearly for both eukaryotic topoII and DNA gyrase. This study is an attempt to understand whether the B subunit of DNA gyrase binds to DNA directly, which may be central to the stimulation of its ATPase activity essential for gyrase function. We have dissected the Plasmodium falciparum gyrase B (PfGyrB) subunit to identify a 45-amino-acid region in the toprim domain that is responsible for its intrinsic DNA binding activity, DNA-stimulated ATPase activity, and DNA cleavage. We find that DNA has to enter through the ATP-operated clamp of PfGyrB to gain access to the DNA binding region. Furthermore, the rate of ATP hydrolysis of PfGyrB increases significantly with increasing DNA length, suggesting a possible communication between the ATPase domain and the DNA binding region that can account for its optimal ATPase activity. These results not only highlight the mechanism of GyrB action in the deadly human parasite P. falciparum but also provide meaningful insights into the current mechanistic model of DNA transport by gyrase during the topoisomerization reaction.
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26
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Collins TRL, Hammes GG, Hsieh TS. Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective. Nucleic Acids Res 2009; 37:712-20. [PMID: 19155278 PMCID: PMC2647300 DOI: 10.1093/nar/gkn1059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Type II DNA topoisomerases (topos) are essential and ubiquitous enzymes that perform important intracellular roles in chromosome condensation and segregation, and in regulating DNA supercoiling. Eukaryotic topo II, a type II topoisomerase, is a homodimeric enzyme that solves topological entanglement problems by using the energy from ATP hydrolysis to pass one segment of DNA through another by way of a reversible, enzyme-bridged double-stranded break. This DNA break is linked to the protein by a phosphodiester bond between the active site tyrosine of each subunit and backbone phosphate of DNA. The opening and closing of the DNA gate, a critical step for strand passage during the catalytic cycle, is coupled to this enzymatic cleavage/religation of the backbone. This reversible DNA cleavage reaction is the target of a number of anticancer drugs, which can elicit DNA damage by affecting the cleavage/religation equilibrium. Because of its clinical importance, many studies have sought to determine the manner in which topo II interacts with DNA. Here we highlight recent single-molecule fluorescence resonance energy transfer and crystallographic studies that have provided new insight into the dynamics and structure of the topo II DNA gate.
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Affiliation(s)
- Tammy R L Collins
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Yang SY, Jia XZ, Feng LY, Li SY, An GS, Ni JH, Jia HT. Inhibition of topoisomerase II by 8-chloro-adenosine triphosphate induces DNA double-stranded breaks in 8-chloro-adenosine-exposed human myelocytic leukemia K562 cells. Biochem Pharmacol 2008; 77:433-43. [PMID: 19014910 DOI: 10.1016/j.bcp.2008.10.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/21/2008] [Accepted: 10/21/2008] [Indexed: 11/15/2022]
Abstract
8-Chloro-cAMP and 8-chloro-adenosine (8-Cl-Ado) are known to inhibit proliferation of cancer cells by converting 8-Cl-Ado into an ATP analog, 8-chloro-ATP (8-Cl-ATP). Because type II topoisomerases (Topo II) are ATP-dependent, we infer that 8-Cl-Ado exposure might interfere with Topo II activities and DNA metabolism in cells. We found that 8-Cl-Ado exposure inhibited Topo II-catalytic activities in K562 cells, as revealed by decreased relaxation of the supercoiled pUC19 DNA and inhibited decatenation of the kinetoplast DNA (kDNA). In vitro assays showed that 8-Cl-ATP, but not 8-Cl-Ado, could directly inhibit Topo IIalpha-catalyzed relaxation and decatenation of substrate DNA. Furthermore, 8-Cl-ATP inhibited Topo II-catalyzed ATP hydrolysis and increased salt-stabilized closed clamp. In addition, 8-Cl-Ado exposure decreased bromo-deoxyuridine (BrdU) incorporation into DNA and led to enhanced DNA double-stranded breaks (DSBs) and to increased formation of gamma-H2AX nuclear foci in exposed K562 cells. Together, 8-Cl-Ado/8-Cl-ATP can inhibit Topo II activities in cells, thereby inhibiting DNA synthesis and inducing DNA DSBs, which may contribute to 8-Cl-Ado-inhibited proliferation of cancers.
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Affiliation(s)
- Sheng-Yong Yang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Xue Yuan Road 38, Beijing 100083, PR China
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Mueller-Planitz F, Herschlag D. Coupling between ATP binding and DNA cleavage by DNA topoisomerase II: A unifying kinetic and structural mechanism. J Biol Chem 2008; 283:17463-76. [PMID: 18403371 DOI: 10.1074/jbc.m710014200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA topoisomerase II is a molecular machine that couples ATP hydrolysis to the transport of one DNA segment through a transient break in another segment. To learn about the energetic connectivity that underlies this coupling, we investigated how the ATPase domains exert control over DNA cleavage. We dissected the DNA cleavage reaction by measuring rate and equilibrium constants for the individual reaction steps utilizing defined DNA duplexes in the presence and absence of the nonhydrolyzable ATP analog 5'-adenylyl-beta,gamma-imidodiphosphate (AMPPNP). Our results revealed the existence of two enzyme conformations whose relative abundance is sensitive to the presence of nucleotides. The predominant species in the absence of nucleotides binds DNA at a diffusion limited rate but cannot efficiently cleave DNA. In the presence of AMPPNP, most of the enzyme is converted to a state in which DNA binding and release is extremely slow but which allows DNA cleavage. A minimal kinetic and thermodynamic framework is established that accounts for the cooperativity of cleavage of the two DNA strands in the presence and absence of bound AMPPNP and includes conformational steps revealed in the kinetic studies. The model unifies available kinetic, thermodynamic, and structural data to provide a description for the reaction in terms of the order and rate of individual reaction steps and the physical nature of the species on the reaction path. Furthermore, this reaction framework provides a foundation for a future in-depth analysis of energy transduction by topoisomerase II, for guiding and interpreting future structural studies, and for analyzing the mechanism of drugs that convert topoisomerase into a cellular poison.
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Affiliation(s)
- Felix Mueller-Planitz
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305, USA
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Qin Y, Meng L, Hu C, Duan W, Zuo Z, Lin L, Zhang X, Ding J. Gambogic acid inhibits the catalytic activity of human topoisomerase IIalpha by binding to its ATPase domain. Mol Cancer Ther 2007; 6:2429-40. [PMID: 17876042 DOI: 10.1158/1535-7163.mct-07-0147] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study is intended to characterize the cellular target of gambogic acid (GA), a natural product isolated from the gamboge resin of Garcinia hurburyi tree, which possesses potent in vitro and in vivo antitumor activities. The antiproliferative activity of GA was further confirmed here in a panel of human tumor cells and multidrug-resistant cells. We found that GA significantly inhibited the catalytic activity of topoisomerase (Topo) II and, to a comparatively less extent, of Topo I, without trapping and stabilizing covalent topoisomerase-DNA cleavage complexes. Down-regulation of Topo IIalpha but not Topo I and Topo IIbeta, reduced GA-induced apoptosis and the phosphorylation of c-Jun, and restored cell proliferation upon GA treatment. Moreover, GA antagonized etoposide-induced DNA damage and abrogated the antiproliferative activity of etoposide, whereas it did not affect camptothecin-induced DNA damage. By dissecting the actions of GA on the individual steps of Topo IIalpha catalytic cycle, we found that GA inhibited DNA cleavage and ATP hydrolysis. Moreover, GA directly bound to the ATPase domain of Topo IIalpha, and may share common binding sites with ATP. The results reported here show that GA exerts its antiproliferative effect by inhibiting the catalytic activity Topo IIalpha. They also indicate that GA inhibits Topo IIalpha-mediated DNA cleavage and modulate the activity of Topo II poisons, which provide rationale for further clinical evaluation of GA.
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Affiliation(s)
- Yuxin Qin
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, PR China
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Nur-E-Kamal A, Meiners S, Ahmed I, Azarova A, Lin CP, Lyu YL, Liu LF. Role of DNA topoisomerase IIβ in neurite outgrowth. Brain Res 2007; 1154:50-60. [PMID: 17493591 DOI: 10.1016/j.brainres.2007.04.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 03/26/2007] [Accepted: 04/03/2007] [Indexed: 10/23/2022]
Abstract
Failure to establish neuromuscular junctions is a major phenotype of top2beta knockout mice. However, the precise mechanism for this defect is not known. In the current study, we have investigated the role of TopIIbeta in cultured neurons. We showed that the TopII inhibitor ICRF-193 significantly blocked neurite outgrowth and growth cone formation in cultured cerebellar granule neurons (CGNs), dorsal root ganglions (DRGs) and cortical neurons (CNs). In addition, ICRF-193 also blocked neurite outgrowth and growth cone formation of PC12 cells undergoing NGF-induced differentiation. Isolated cortical neurons from top2beta knockout embryos elaborated shorter neurites than did those from their wild type counterparts, confirming the role of TopIIbeta in neurite outgrowth. Together, these results demonstrate a critical role of TopIIbeta in neurite outgrowth in cultured neurons. Furthermore, we demonstrated that neurons derived from top2beta knockout mice failed to form contacts with muscle cells in co-cultures. These results suggest that the defect in establishing neuromuscular junctions in top2beta knockout mice could be due to the lack of TopIIbeta-mediated neurite outgrowth.
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Affiliation(s)
- Alam Nur-E-Kamal
- Department of Biology, MEC-CUNY, 1150 Carroll Street, Brooklyn, NY 11225, USA.
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Smiley RD, Collins TRL, Hammes GG, Hsieh TS. Single-molecule measurements of the opening and closing of the DNA gate by eukaryotic topoisomerase II. Proc Natl Acad Sci U S A 2007; 104:4840-5. [PMID: 17360343 PMCID: PMC1829226 DOI: 10.1073/pnas.0700342104] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type II DNA topoisomerases are essential and ubiquitous enzymes that perform important functions in chromosome condensation and segregation and in regulating intracellular DNA supercoiling. Topoisomerases carry out these DNA transactions by passing one segment of DNA through the other by using a reversible, enzyme-bridged double strand break. The transient enzyme/DNA adduct is mediated by a phosphodiester bond between the active-site tyrosine and a backbone phosphate of DNA. The opening and closing of the DNA gate, a critical step for strand passage during the catalytic cycle, is coupled to this cleavage/religation. We designed a unique oligonucleotide substrate with a pair of fluorophores straddling the topoisomerase II cleavage site, allowing the use of FRET to monitor the opening of the DNA gate. The DNA substrate undergoes an enzyme-mediated transition between a closed and open state in the presence of ATP, similar to the overall topoisomerase II catalyzed reaction. Single-molecule fluorescence microscopy measurements demonstrate that the transition has comparable rate constants for both the opening and closing reaction during steady-state ATP hydrolysis, with an apparent equilibrium constant near unity. In the presence of AMPPNP, a reduction in FRET occurs, suggesting an opening or partial opening of the DNA gate. However, the single-molecule experiments indicate that the open and closed states do not interconvert at a measurable rate.
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Affiliation(s)
- R. Derike Smiley
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Tammy R. L. Collins
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
| | - Gordon G. Hammes
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
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32
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Zhu H, Huang M, Yang F, Chen Y, Miao ZH, Qian XH, Xu YF, Qin YX, Luo HB, Shen X, Geng MY, Cai YJ, Ding J. R16, a novel amonafide analogue, induces apoptosis and G2-M arrest via poisoning topoisomerase II. Mol Cancer Ther 2007; 6:484-95. [PMID: 17308047 DOI: 10.1158/1535-7163.mct-06-0584] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Amonafide, a naphthalimide derivative, although selected for exploratory clinical trials for its potent anticancer activity, has long been challenged by its unpredictable side effects. In the present study, a novel amonafide analogue, 2-(2-dimethylamino)-6-thia-2-aza-benzo-[def]-chrysene-1,3-diones (R16) was synthesized by substituting 5'-NH(2) of the naphthyl with a heterocyclic group to amonafide, with additional introduction of a thiol group. In a panel of various human tumor cell lines, R16 was more cytotoxic than its parent compound amonafide. It was also effective against multidrug-resistant cells. Importantly, the i.p. administration of R16 inhibited tumor growth in mice implanted with S-180 sarcoma and H(22) hepatoma. The molecular and cellular machinery studies showed that the R16 functions as a topoisomerase II (topo II) poison via binding to the ATPase domain of human topo IIalpha. The superior cytotoxicity of R16 to amonafide was ascribed to its potent effects on trapping topo II-DNA cleavage complexes. Moreover, using a topo II catalytic inhibitor aclarubicin, ataxia-telangiectasia-mutated (ATM)/ATM- and Rad3-related (ATR) kinase inhibitor caffeine and topo II-deficient HL-60/MX2 cells, we further showed that R16-triggered DNA double-strand breaks, tumor cell cycle arrest, and apoptosis were in a topo II-dependent manner. Taken together, R16 stood out by its improved anticancer activity, appreciable anti-multidrug resistance activities, and well-defined topo II poisoning mechanisms, as comparable with the parent compound amonafide. All these collectively promise the potential value of R16 as an anticancer drug candidate, which deserves further development.
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Affiliation(s)
- Hong Zhu
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, P.R. China
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33
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Hu CX, Zuo ZL, Xiong B, Ma JG, Geng MY, Lin LP, Jiang HL, Ding J. Salvicine functions as novel topoisomerase II poison by binding to ATP pocket. Mol Pharmacol 2006; 70:1593-601. [PMID: 16914642 DOI: 10.1124/mol.106.027714] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salvicine, a structurally modified diterpenoid quinone derived from Salvia prionitis, is a nonintercalative topoisomerase II (topo II) poison. The compound possesses potent in vitro and in vivo antitumor activity with a broad spectrum of anti-multidrug resistance activity and is currently in phase II clinical trials. To elucidate the distinct antitumor properties of salvicine and obtain valuable structural information of salvicine-topo II interactions, we characterized the effects of salvicine on human topo IIalpha (htopo IIalpha), including possible binding sites and molecular interactions. The enzymatic assays disclosed that salvicine mainly inhibits the catalytic activity with weak DNA cleavage action, in contrast to the classic topo II poison etoposide (VP16). Molecular modeling studies predicted that salvicine binds to the ATP pocket in the ATPase domain and superimposes on the phosphate and ribose groups. In a surface plasmon resonance binding assay, salvicine exhibited higher affinity for the ATPase domain of htopo IIalpha than ATP and ADP. Competitive inhibition tests demonstrated that ATP competitively and dose-dependently blocked the interactions between salvicine and ATPase domain of htopo IIalpha. The data illustrate that salvicine shares a common binding site with ATP and functions as an ATP competitor. To our knowledge, this is the first report to identify an ATP-binding pocket as the structural binding motif for a nonintercalative eukaryotic topo II poison. These findings collectively support the potential value of an ATP competitor of htopo IIalpha in tumor chemotherapy.
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MESH Headings
- Adenosine Triphosphatases/isolation & purification
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/metabolism
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/metabolism
- Antineoplastic Agents, Phytogenic/pharmacology
- Binding Sites
- Catalysis
- DNA/chemistry
- DNA Topoisomerases, Type II/chemistry
- DNA Topoisomerases, Type II/metabolism
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/chemistry
- DNA-Binding Proteins/metabolism
- Dose-Response Relationship, Drug
- Humans
- Hydrolysis
- Models, Molecular
- Naphthoquinones/chemistry
- Naphthoquinones/metabolism
- Naphthoquinones/pharmacology
- Nucleic Acid Conformation
- Protein Structure, Tertiary
- Topoisomerase II Inhibitors
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Affiliation(s)
- Chao-Xin Hu
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
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34
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Mueller-Planitz F, Herschlag D. Interdomain communication in DNA topoisomerase II. DNA binding and enzyme activation. J Biol Chem 2006; 281:23395-404. [PMID: 16782968 DOI: 10.1074/jbc.m604119200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerase II catalyzes the ATP-dependent transport of a DNA segment (T-DNA) through a transient double strand break in another DNA segment (G-DNA). A fundamental mechanistic question is how the individual steps in this process are coordinated. We probed communication between the DNA binding sites and the individual enzymatic activities, ATP hydrolysis, and DNA cleavage. We employed short DNA duplexes to control occupancy at the two binding sites of wild-type enzyme and a variant with a G-DNA site mutation. The DNA concentration dependence of ATP hydrolysis and a fluorescence anisotropy assay provided thermodynamic information about DNA binding. The results suggest that G-DNA binds with higher affinity than T-DNA. Enzyme with only G-DNA bound is competent to cleave DNA, indicating that T-DNA is dispensable for DNA cleavage. The ATPase activity of enzyme bound solely to G-DNA is partially stimulated. Full stimulation requires binding of T-DNA. Both DNA binding sites therefore signal to the ATPase domains. The results support and extend current mechanistic models for topoisomerase II-catalyzed DNA transport and provide a framework for future mechanistic dissection.
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Affiliation(s)
- Felix Mueller-Planitz
- Department of Biochemistry, School of Medicine, Stanford University, Stanford, California 94305-5307, USA
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35
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Sengupta T, Mukherjee M, Das A, Mandal C, Das R, Mukherjee T, Majumder H. Characterization of the ATPase activity of topoisomerase II from Leishmania donovani and identification of residues conferring resistance to etoposide. Biochem J 2006; 390:419-26. [PMID: 15901238 PMCID: PMC1198921 DOI: 10.1042/bj20042128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have cloned and expressed the 43 kDa N-terminal domain of Leishmania donovani topoisomerase II. This protein has an intrinsic ATPase activity and obeys Michaelis-Menten kinetics. Cross-linking studies indicate that the N-terminal domain exists as a dimer both in the presence and absence of nucleotides. Etoposide, an effective antitumour drug, traps eukaryotic DNA topoisomerase II in a covalent complex with DNA. In the present study, we report for the first time that etoposide inhibits the ATPase activity of the recombinant N-terminal domain of L. donovani topoisomerase II. We have modelled the structure of this 43 kDa protein and performed molecular docking analysis with the drug. Mutagenesis of critical amino acids in the vicinity of the ligand-binding pocket reveals less efficient inhibition of the ATPase activity of the enzyme by etoposide. Taken together, these results provide an insight for the development of newer therapeutic agents with specific selectivity.
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Affiliation(s)
- Tanushri Sengupta
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Mandira Mukherjee
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Aditi Das
- †Sealy Center for Molecular Sciences, University of Texas Medical Branch at Galveston, Galveston, TX-77555, U.S.A
| | - Chhabinath Mandal
- ‡Department of Drug Design, Development and Molecular Modeling, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Rakhee Das
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Tanmoy Mukherjee
- §Infectious Disease Group, Indian Institute of Chemical Biology, Kolkata-700032, India
| | - Hemanta K. Majumder
- *Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata-700032, India
- To whom correspondence should be addressed (email )
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36
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Corbett KD, Berger JM. Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure 2005; 13:873-82. [PMID: 15939019 DOI: 10.1016/j.str.2005.03.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 03/12/2005] [Accepted: 03/21/2005] [Indexed: 11/25/2022]
Abstract
GHL proteins are functionally diverse enzymes defined by the presence of a conserved ATPase domain that self-associates to trap substrate upon nucleotide binding. The structural states adopted by these enzymes during nucleotide hydrolysis and product release, and their consequences for enzyme catalysis, have remained unclear. Here, we have determined a complete structural map of the ATP turnover cycle for topoVI-B, the ATPase subunit of the archaeal GHL enzyme topoisomerase VI. With this ensemble of structures, we show that significant conformational changes in the subunit occur first upon ATP binding, and subsequently upon release of hydrolyzed P(i). Together, these data provide a structural framework for understanding the role of ATP hydrolysis in the type II topoisomerase reaction. Our results also suggest that the GHL ATPase module is a molecular switch in which ATP hydrolysis serves as a prerequisite but not a driving force for substrate-dependent structural transitions in the enzyme.
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Affiliation(s)
- Kevin D Corbett
- Department of Molecular and cellular biology, University of California, Berkeley, California 94720, USA
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37
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Wei H, Ruthenburg AJ, Bechis SK, Verdine GL. Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. J Biol Chem 2005; 280:37041-7. [PMID: 16100112 DOI: 10.1074/jbc.m506520200] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type IIA DNA topoisomerases play multiple essential roles in the management of higher-order DNA structure, including modulation of topological state, chromosome segregation, and chromatin condensation. These diverse physiologic functions are all accomplished through a common molecular mechanism, wherein the protein catalyzes transient cleavage of a DNA duplex (the G-segment) to yield a double-stranded gap through which another duplex (the T-segment) is passed. The overall process is orchestrated by the opening and closing of molecular "gates" in the topoisomerase structure, which is regulated by ATP binding, hydrolysis, and release of ADP and inorganic phosphate. Here we present two crystal structures of the ATPase domain of human DNA topoisomerase IIalpha in different nucleotide-bound states. Comparison of these structures revealed rigid-body movement of the structural modules within the ATPase domain, suggestive of the motions of a molecular gate.
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Affiliation(s)
- Hua Wei
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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38
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Khor V, Yowell C, Dame JB, Rowe TC. Expression and characterization of the ATP-binding domain of a malarial Plasmodium vivax gene homologous to the B-subunit of the bacterial topoisomerase DNA gyrase. Mol Biochem Parasitol 2005; 140:107-17. [PMID: 15694492 DOI: 10.1016/j.molbiopara.2004.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Accepted: 12/16/2004] [Indexed: 10/25/2022]
Abstract
We have previously reported the presence of a DNA gyrase-like topoisomerase activity associated with the 35kb apicoplast DNA in the malarial parasite Plasmodium falciparum [Weissig V, Vetro-Widenhouse TS, Rowe TC. Topoisomerase II inhibitors induce cleavage of nuclear and 35kb plastid DNAs in the malarial parasite Plasmodium falciparum. DNA Cell Biol 1997;16:1483]. Sequences encoding polypeptides homologous to both the A and B subunits of bacterial DNA gyrase have been identified in the genome sequence of P. falciparum among data produced by the Malaria Genome Consortium and the University of Florida Malaria Gene Sequence Tag Project. Based on these findings, we have cloned and expressed a region of the Plasmodium vivax GyrB gene encoding a 43kDa polypeptide homologous to the ATP-binding domain of Escherichia coli DNA gyrase. The 43kDa PvGyrB polypeptide was found to have intrinsic ATPase activity with a K(m) of 0.27mM and a k(cat) of 0.051s(-1). The PvGyrB ATPase was also sensitive to the bacterial DNA gyrase inhibitor coumermycin. The implications of these findings are discussed.
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Affiliation(s)
- Victor Khor
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, FL 32610-0267, USA
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39
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McLaughlin SH, Ventouras LA, Lobbezoo B, Jackson SE. Independent ATPase activity of Hsp90 subunits creates a flexible assembly platform. J Mol Biol 2005; 344:813-26. [PMID: 15533447 DOI: 10.1016/j.jmb.2004.09.055] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 08/16/2004] [Accepted: 09/20/2004] [Indexed: 01/06/2023]
Abstract
The ATPase activity of the molecular chaperone Hsp90 is essential for its function in the assembly of client proteins. To understand the mechanism of human Hsp90, we have carried out a detailed kinetic analysis of ATP binding, hydrolysis and product release. ATP binds rapidly in a two-step process involving the formation of a diffusion-collision complex followed by a conformational change. The rate-determining step was shown to be ATP hydrolysis and not subsequent ADP dissociation. There was no evidence from any of the biophysical measurements for cooperativity in either nucleotide binding or hydrolysis for the dimeric protein. A monomeric fragment, lacking the C-terminal dimerisation domain, showed no dependence on protein concentration and, therefore, subunit association for activity. The thermodynamic linkage between client protein binding and nucleotide affinity revealed ATP bound Hsp90 has a higher affinity for client proteins than the ADP bound form. The kinetics are consistent with independent Michaelis-Menten catalysis in each subunit of the Hsp90 dimer. We propose that Hsp90 functions in an open-ring configuration for client protein activation.
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Affiliation(s)
- Stephen H McLaughlin
- Cambridge University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.
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40
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Vaughn J, Huang S, Wessel I, Sorensen TK, Hsieh T, Jensen LH, Jensen PB, Sehested M, Nitiss JL. Stability of the topoisomerase II closed clamp conformation may influence DNA-stimulated ATP hydrolysis. J Biol Chem 2005; 280:11920-9. [PMID: 15647268 DOI: 10.1074/jbc.m411841200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type II DNA topoisomerases catalyze changes in DNA topology and use nucleotide binding and hydrolysis to control conformational changes required for the enzyme reaction. We examined the ATP hydrolysis activity of a bisdioxopiperazine-resistant mutant of human topoisomerase II alpha with phenylalanine substituted for tyrosine at residue 50 in the ATP hydrolysis domain of the enzyme. This substitution reduced the DNA-dependent ATP hydrolysis activity of the mutant protein without affecting the relaxation activity of the enzyme. A similar but stronger effect was seen when the homologous mutation (Tyr28 --> Phe) was introduced in yeast Top2. The ATPase activities of human TOP2alpha(Tyr50 --> Phe) and yeast Top2(Tyr28 --> Phe) were resistant to both bisdioxopiperazines and the ATPase inhibitor sodium orthovanadate. Like bisdioxopiperazines, vanadate traps the enzyme in a salt-stable closed conformation termed the closed clamp, which can be detected in the presence of circular DNA substrates. Consistent with the vanadate-resistant ATPase activity, salt-stable closed clamps were not detected in reactions containing the yeast or human mutant protein, vanadate, and ATP. Similarly, ADP trapped wild-type topoisomerase II as a closed clamp, but could not trap either the human or yeast mutant enzymes. Our results demonstrate that bisdioxopiperazine-resistant mutants exhibit a difference in the stability of the closed clamp formed by the enzyme and that this difference in stability may lead to a loss of DNA-stimulated ATPase. We suggest that the DNA-stimulated ATPase of topoisomerase II is intimately connected with steps that occur while the N-terminal domain of the enzyme is dimerized.
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Affiliation(s)
- Jerrylaine Vaughn
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Immormino RM, Dollins DE, Shaffer PL, Soldano KL, Walker MA, Gewirth DT. Ligand-induced conformational shift in the N-terminal domain of GRP94, an Hsp90 chaperone. J Biol Chem 2004; 279:46162-71. [PMID: 15292259 DOI: 10.1074/jbc.m405253200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GRP94 is the endoplasmic reticulum paralog of cytoplasmic Hsp90. Models of Hsp90 action posit an ATP-dependent conformational switch in the N-terminal ligand regulatory domain of the chaperone. However, crystal structures of the isolated N-domain of Hsp90 in complex with a variety of ligands have yet to demonstrate such a conformational change. We have determined the structure of the N-domain of GRP94 in complex with ATP, ADP, and AMP. Compared with the N-ethylcarboxamidoadenosine and radicicol-bound forms, these structures reveal a large conformational rearrangement in the protein. The nucleotide-bound form exposes new surfaces that interact to form a biochemically plausible dimer that is reminiscent of those seen in structures of MutL and DNA gyrase. Weak ATP binding and a conformational change in response to ligand identity are distinctive mechanistic features of GRP94 and suggest a model for how GRP94 functions in the absence of co-chaperones and ATP hydrolysis.
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Affiliation(s)
- Robert M Immormino
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Vilain N, Tsai-Pflugfelder M, Benoit A, Gasser SM, Leroy D. Modulation of drug sensitivity in yeast cells by the ATP-binding domain of human DNA topoisomerase IIalpha. Nucleic Acids Res 2003; 31:5714-22. [PMID: 14500835 PMCID: PMC206448 DOI: 10.1093/nar/gkg737] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Epipodophyllotoxins are effective antitumour drugs that trap eukaryotic DNA topoisomerase II in a covalent complex with DNA. Based on DNA cleavage assays, the mode of interaction of these drugs was proposed to involve amino acid residues of the catalytic site. An in vitro binding study, however, revealed two potential binding sites for etoposide within human DNA topoisomerase IIalpha (htopoIIalpha), one in the catalytic core of the enzyme and one in the ATP-binding N-terminal domain. Here we have tested how N-terminal mutations that reduce the affinity of the site for etoposide or ATP affect the sensitivity of yeast cells to etoposide. Surprisingly, when introduced into full-length enzymes, mutations that lower the drug binding capacity of the N-terminal domain in vitro render yeast more sensitive to epipodophyllotoxins. Consistently, when the htopoIIalpha N-terminal domain alone is overexpressed in the presence of yeast topoII, cells become more resistant to etoposide. Point mutations that weaken etoposide binding eliminate this resistance phenotype. We argue that the N-terminal ATP-binding pocket competes with the active site of the holoenzyme for binding etoposide both in cis and in trans with different outcomes, suggesting that each topoisomerase II monomer has two non-equivalent drug-binding sites.
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Affiliation(s)
- Nathalie Vilain
- Swiss Institute for Experimental Cancer Research, Ch. des Boveresses 155, CH-1066 Epalinges s/Lausanne, Switzerland
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Classen S, Olland S, Berger JM. Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proc Natl Acad Sci U S A 2003; 100:10629-34. [PMID: 12963818 PMCID: PMC196855 DOI: 10.1073/pnas.1832879100] [Citation(s) in RCA: 199] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Type IIA topoisomerases both manage the topological state of chromosomal DNA and are the targets of a variety of clinical agents. Bisdioxopiperazines are anticancer agents that associate with ATP-bound eukaryotic topoisomerase II (topo II) and convert the enzyme into an inactive, salt-stable clamp around DNA. To better understand both topo II and bisdioxopiperazine function, we determined the structures of the adenosine 5'-[beta,gamma-imino]-triphosphate-bound yeast topo II ATPase region (ScT2-ATPase) alone and complexed with the bisdioxopiperazine ICRF-187. The drug-free form of the protein is similar in overall fold to the equivalent region of bacterial gyrase but unexpectedly displays significant conformational differences. The ternary drug-bound complex reveals that ICRF-187 acts by an unusual mechanism of inhibition in which the drug does not compete for the ATP-binding pocket, but bridges and stabilizes a transient dimer interface between two ATPase protomers. Our data explain why bisdioxopiperazines target ATP-bound topo II, provide a structural rationale for the effects of certain drug-resistance mutations, and point to regions of bisdioxopiperazines that might be modified to improve or alter drug specificity.
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Affiliation(s)
- Scott Classen
- Department of Molecular and Cell Biology, 237 Hildebrand Hall, University of California, Berkeley, CA 94720-3206, USA
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Abstract
The nuclear enzyme DNA topoisomerase II is a major target for antineoplastic agents. All topoisomerase II-directed agents are able to interfere with at least one step of the catalytic cycle. Agents able to stabilize the covalent DNA topoisomerase II complex (also known as the cleavable complex) are traditionally called topoisomerase II poisons, while agents acting on any of the other steps in the catalytic cycle are called catalytic inhibitors. Thus, catalytic topoisomerase II inhibitors are a heterogeneous group of compounds that might interfere with the binding between DNA and topoisomerase II (aclarubicin and suramin), stabilize noncovalent DNA topoisomerase II complexes (merbarone, ICRF-187, and structurally related bisdioxopiperazine derivatives), or inhibit ATP binding (novobiocin). Some, such as fostriecin, may also have alternative biological targets. Whereas topoisomerase II poisons are used solely for their antitumor activities, catalytic inhibitors are utilized for a variety of reasons, including their activity as antineoplastic agents (aclarubicin and MST-16), cardioprotectors (ICRF-187), or modulators in order to increase the efficacy of other agents (suramin and novobiocin). In this review, the mechanism and biological activity of different catalytic inhibitors is described, with emphasis on therapeutically used compounds. We will then discuss future development and applications of this interesting class of compounds.
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Affiliation(s)
- Annette K Larsen
- CNRS UMR 8532, Ecole Normale Supérieure, Cachan and Institut Gustave Roussy PR2, 94805 Villejuif, France.
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Umemura K, Yanase K, Suzuki M, Okutani K, Yamori T, Andoh T. Inhibition of DNA topoisomerases I and II, and growth inhibition of human cancer cell lines by a marine microalgal polysaccharide. Biochem Pharmacol 2003; 66:481-7. [PMID: 12907247 DOI: 10.1016/s0006-2952(03)00281-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have previously reported purification of an extracellular polysaccharide GA3P, D-galactan sulfate associated with L-(+)-lactic acid, produced by a toxic marine microalga Dinoflagellate Gymnodinium sp. A(3) (GA3), and induction thereby of apoptosis on human myeloid leukemia K562 cells. In the present report, we show that the GA3P is a potent inhibitor of DNA topoisomerase (topo) I and topo II, irrespective of the presence or absence of the lactate group. Dextran sulfate also showed similar level of inhibition of topo I and topo II. We also demonstrated that, unlike camptothecin (CPT) or teniposide (VM-26), the inhibition of topo I or topo II by the polysaccharide does not involve accumulation of DNA-topo I/II cleavable complexes, clearly showing that they are not topo poisons but catalytic inhibitors with dual activity. Furthermore, the polysaccharide, when added to the reaction mixture with CPT or VM-26, inhibited stabilization of cleavable complex induced by the latter compounds. In addition, when added to the reaction mixture after the formation of the cleavable complexes by topo poisons, CPT for topo I and VM-26 for topo II, either GA3P or dextran sulfate diminished the amount of the complexes already accumulated, i.e. reversal of the reaction. These results suggest that the polysaccharides bind to the enzymes with high affinities, and that, as for topo I/II inhibition, the GA3P shares a common mechanism with dextran sulfate. As examined in vitro with a human cancer cell line panel, GA3P exhibited significant cytotoxicity against a variety of cancer cells. These findings show that the polysaccharide GA3P would prove to be a potential anticancer chemotherapeutic agent with dual activity of topo I and topo II catalytic inhibition.
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Affiliation(s)
- Ken Umemura
- Department of Bioengineering, Faculty of Engineering, Soka University, 1-236 Tangi-machi, Hachiouji, Tokyo 192-8577, Japan
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Renodon-Cornière A, Sørensen TK, Jensen PB, Nitiss JL, Søkilde B, Sehested M, Jensen LH. Probing the role of linker substituents in bisdioxopiperazine analogs for activity against wild-type and mutant human topoisomerase II alpha. Mol Pharmacol 2003; 63:1159-68. [PMID: 12695544 DOI: 10.1124/mol.63.5.1159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The bisdioxopiperazines are catalytic inhibitors of eukaryotic type II DNA topoisomerases capable of trapping these enzymes as a salt-stable closed-clamp complex on circular DNA. The various bisdioxopiperazine analogs differ from each other because of structural differences in the linker connecting the two dioxopiperazine rings. Although the composition of this linker region has been found to be important for potency, the structural basis for this is largely unknown. To elucidate the role of the linker region in drug action, we have analyzed the effect of different linker substituents in otherwise identical analogs by studying their interaction with wild-type and mutant human topoisomerase II alpha. Two mutations, L169I and R162Q, displayed differential sensitivity toward closely related analogs, suggesting that the linker region in these compounds plays a highly specific role in protein drug interaction. The finding that the L169I mutation, which probably represents a subtle structural change, was sufficient to confer resistance further emphases the importance of this region of the protein for bisdioxopiperazine inhibition of topoisomerase II. Comparing the sensitivity profiles of different bisdioxopiperazines against wild-type and mutant proteins with that of mitindomide, we observed a spectrum of sensitivity closely resembling that of ICRF-154, a bisdioxopiperazine with no linker substituents. We discuss the implications of these observations for the understanding of the mechanism of bisdioxopiperazine action on topoisomerase II.
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West KL, Turnbull RM, Willmore E, Lakey JH, Austin CA. Characterisation of the DNA-dependent ATPase activity of human DNA topoisomerase IIbeta: mutation of Ser165 in the ATPase domain reduces the ATPase activity and abolishes the in vivo complementation ability. Nucleic Acids Res 2002; 30:5416-24. [PMID: 12490710 PMCID: PMC140051 DOI: 10.1093/nar/gkf677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report for the first time an analysis of the ATPase activity of human DNA topoisomerase (topo) IIbeta. We show that topo IIbeta is a DNA-dependent ATPase that appears to fit Michaelis-Menten kinetics. The ATPase activity is stimulated 44-fold by DNA. The k(cat) for ATP hydrolysis by human DNA topo IIbeta in the presence of DNA is 2.25 s(-1). We have characterised a topo IIbeta derivative which carries a mutation in the ATPase domain (S165R). S165R reduced the kcat for ATP hydrolysis by 7-fold, to 0.32 s(-1), while not significantly altering the apparent K(m). The specificity constant for the interaction between ATP and topo IIbeta (kcat/K(mapp)) showed a 90% reduction for betaS165R. The DNA binding affinity and ATP-independent DNA cleavage activity of the enzyme are unaffected by this mutation. However, the strand passage activity is reduced by 80%, presumably due to reduced ATP hydrolysis. The mutant enzyme is unable to complement ts yeast topo II in vivo. We have used computer modelling to predict the arrangement of key residues at the ATPase active site of topo IIbeta. Ser165 is predicted to lie very close to the bound nucleotide, and the S165R mutation could thus influence both ATP binding and ADP dissociation.
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Affiliation(s)
- Katherine L West
- School of Cell and Molecular BioSciences, The Medical School, The University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK
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Abstract
ATPases are involved in several cellular functions, and are at the origin of various human diseases. They are therefore attractive drug targets, and various ATPase inhibitors are already on the market. However, most of these drugs are active without binding directly to the nucleotide-binding site. An alternative strategy to inhibit ATPases is to design competitive ATP inhibitors. This approach, which has been used successfully to design protein-kinase inhibitors, depends on the structure of the nucleotide-binding site. This review describes the structural features of the nucleotide-binding site of various ATPases and analyses how this structural information can be exploited for drug discovery.
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Affiliation(s)
- Patrick Chène
- Oncology Department, Novartis, K125 442, CH-4002 Basel, Switzerland.
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Campbell S, Maxwell A. The ATP-operated clamp of human DNA topoisomerase IIalpha: hyperstimulation of ATPase by "piggy-back" binding. J Mol Biol 2002; 320:171-88. [PMID: 12079377 DOI: 10.1016/s0022-2836(02)00461-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have constructed a series of clones encoding N-terminal fragments of human DNA topoisomerase IIalpha. All fragments exhibit DNA-dependent ATPase activity. Fragment 1-420 shows hyperbolic dependence of ATPase on DNA concentration, whereas fragment 1-453 shows hyperstimulation at low ratios of DNA to enzyme, a phenomenon found previously with the full-length enzyme. The minimum length of DNA found to stimulate the ATPase activity was approximately 10 bp; fragments >or=32 bp manifest the hyperstimulation phenomenon. Molecular mass studies show that fragment 1-453 is a monomer in the absence of nucleotides and a dimer in the presence of nucleotide triphosphate. The results are consistent with the role of the N-terminal domain of topoisomerase II as an ATP-operated clamp that dimerises in the presence of ATP. The hyperstimulation effect can be interpreted in terms of a "piggy-back binding" model for protein-DNA interaction.
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Affiliation(s)
- Spencer Campbell
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK
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