101
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Abstract
Covalent DNA-protein crosslinks (DPCs, also known as protein adducts) of topoisomerases and other proteins with DNA are highly toxic DNA lesions. Of note, chemical agents that induce DPCs include widely used classes of chemotherapeutics. Their bulkiness blocks virtually every chromatin-based process and makes them intractable for repair by canonical repair pathways. Distinct DPC repair pathways employ unique points of attack and are crucial for the maintenance of genome stability. Tyrosyl-DNA phosphodiesterases (TDPs) directly hydrolyse the covalent linkage between protein and DNA. The MRE11-RAD50-NBS1 (MRN) nuclease complex targets the DNA component of DPCs, excising the fragment affected by the lesion, whereas proteases of the spartan (SPRTN)/weak suppressor of SMT3 protein 1 (Wss1) family target the protein component. Loss of these pathways renders cells sensitive to DPC-inducing chemotherapeutics, and DPC repair pathways are thus attractive targets for combination cancer therapy.
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Affiliation(s)
- Julian Stingele
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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102
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Wang P, Elsayed MSA, Plescia CB, Ravji A, Redon CE, Kiselev E, Marchand C, Zeleznik O, Agama K, Pommier Y, Cushman M. Synthesis and Biological Evaluation of the First Triple Inhibitors of Human Topoisomerase 1, Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), and Tyrosyl-DNA Phosphodiesterase 2 (Tdp2). J Med Chem 2017; 60:3275-3288. [PMID: 28418653 DOI: 10.1021/acs.jmedchem.6b01565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tdp1 and Tdp2 are two tyrosyl-DNA phosphodiesterases that can repair damaged DNA resulting from topoisomerase inhibitors and a variety of other DNA-damaging agents. Both Tdp1 and Tdp2 inhibition could hypothetically potentiate the cytotoxicities of topoisomerase inhibitors. This study reports the successful structure-based design and synthesis of new 7-azaindenoisoquinolines that act as triple inhibitors of Top1, Tdp1, and Tdp2. Enzyme inhibitory data and cytotoxicity data from human cancer cell cultures establish that modification of the lactam side chain of the 7-azaindenoisoquinolines can modulate their inhibitory potencies and selectivities vs Top1, Tdp1, and Tdp2. Molecular modeling of selected target compounds bound to Top1, Tdp1, and Tdp2 was used to design the inhibitors and facilitate the structure-activity relationship analysis. The monitoring of DNA damage by γ-H2AX foci formation in human PBMCs (lymphocytes) and acute lymphoblastic leukemia CCRF-CEM cells documented significantly more DNA damage in the cancer cells vs normal cells.
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Affiliation(s)
- Ping Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Mohamed S A Elsayed
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Caroline B Plescia
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Azhar Ravji
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Christophe E Redon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Olga Zeleznik
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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103
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Gadd MS, Testa A, Lucas X, Chan KH, Chen W, Lamont DJ, Zengerle M, Ciulli A. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat Chem Biol 2017; 13:514-521. [PMID: 28288108 PMCID: PMC5392356 DOI: 10.1038/nchembio.2329] [Citation(s) in RCA: 680] [Impact Index Per Article: 97.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/27/2017] [Indexed: 12/20/2022]
Abstract
Inducing macromolecular interactions with small molecules to activate cellular signaling
is a challenging goal. PROTACs (proteolysis-targeting chimaeras) are
bifunctional molecules that recruit a target protein in proximity to an E3
ubiquitin ligase to trigger protein degradation. Structural elucidation of the
key ternary ligase:PROTAC:target species and how this impacts target degradation
selectivity remains elusive. We solved the crystal structure of Brd4-degrader
MZ1 in complex with human VHL and the Brd4 bromodomain (Brd4BD2). The
ligand folds into itself to allow formation of specific intermolecular
interactions in the ternary complex. Isothermal titration calorimetry studies,
supported by surface mutagenesis and proximity assays, are consistent with
pronounced cooperative formation of ternary complexes with Brd4BD2.
Structure-based-designed compound AT1 exhibits highly selective depletion of
Brd4 in cells. Our results elucidate how PROTAC-induced de novo
contacts dictate preferential recruitment of a target protein into a stable and
cooperative complex with an E3 ligase for selective degradation.
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Affiliation(s)
- Morgan S Gadd
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Xavier Lucas
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Kwok-Ho Chan
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Wenzhang Chen
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Douglas J Lamont
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Michael Zengerle
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK
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104
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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105
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Infante Lara L, Sledge A, Laradji A, Okoro CO, Osheroff N. Novel trifluoromethylated 9-amino-3,4-dihydroacridin-1(2H)-ones act as covalent poisons of human topoisomerase IIα. Bioorg Med Chem Lett 2016; 27:586-589. [PMID: 27998679 DOI: 10.1016/j.bmcl.2016.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
A number of topoisomerase II-targeted anticancer drugs, including amsacrine, utilize an acridine or related aromatic core as a scaffold. Therefore, to further explore the potential of acridine-related compounds to act as topoisomerase II poisons, we synthesized a series of novel trifluoromethylated 9-amino-3,4-dihydroacridin-1(2H)-one derivatives and examined their ability to enhance DNA cleavage mediated by human topoisomerase IIα. Derivatives containing a H, Cl, F, and Br at C7 enhanced enzyme-mediated double-stranded DNA cleavage ∼5.5- to 8.5-fold over baseline, but were less potent than amsacrine. The inclusion of an amino group at C9 was critical for activity. The compounds lost their activity against topoisomerase IIα in the presence of a reducing agent, displayed no activity against the catalytic core of topoisomerase IIα, and inhibited DNA cleavage when incubated with the enzyme prior to the addition of DNA. These findings strongly suggest that the compounds act as covalent, rather than interfacial, topoisomerase II poisons.
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Affiliation(s)
- Lorena Infante Lara
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Alexis Sledge
- Department of Chemistry, Tennessee State University, Nashville, TN 37209-1561, USA
| | - Amine Laradji
- Department of Chemistry, Tennessee State University, Nashville, TN 37209-1561, USA
| | - Cosmas O Okoro
- Department of Chemistry, Tennessee State University, Nashville, TN 37209-1561, USA.
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
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106
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Moschetti T, Sharpe T, Fischer G, Marsh ME, Ng HK, Morgan M, Scott DE, Blundell TL, R. Venkitaraman A, Skidmore J, Abell C, Hyvönen M. Engineering Archeal Surrogate Systems for the Development of Protein-Protein Interaction Inhibitors against Human RAD51. J Mol Biol 2016; 428:4589-4607. [PMID: 27725183 PMCID: PMC5117717 DOI: 10.1016/j.jmb.2016.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets for small-molecule inhibitor discovery and to exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. As human RAD51 has proved impossible to produce in a form that is compatible with the requirements of fragment-based drug discovery, we have developed a surrogate protein system using RadA from Pyrococcus furiosus. Using a monomerised RadA as our starting point, we have adopted two parallel and mutually instructive approaches to mimic the human enzyme: firstly by mutating RadA to increase sequence identity with RAD51 in the BRC repeat binding sites, and secondly by generating a chimeric archaeal human protein. Both approaches generate proteins that interact with a fourth BRC repeat with affinity and stoichiometry comparable to human RAD51. Stepwise humanisation has also allowed us to elucidate the determinants of RAD51 binding to BRC repeats and the contributions of key interacting residues to this interaction. These surrogate proteins have enabled the development of biochemical and biophysical assays in our ongoing fragment-based small-molecule inhibitor programme and they have allowed us to determine hundreds of liganded structures in support of our structure-guided design process, demonstrating the feasibility and advantages of using archeal surrogates to overcome difficulties in handling human proteins.
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Affiliation(s)
- Tommaso Moschetti
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Timothy Sharpe
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - May E. Marsh
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Hong Kin Ng
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthew Morgan
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Duncan E. Scott
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Ashok R. Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - John Skidmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,Corresponding author.
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107
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Riddell IA, Agama K, Park GY, Pommier Y, Lippard SJ. Phenanthriplatin Acts As a Covalent Poison of Topoisomerase II Cleavage Complexes. ACS Chem Biol 2016; 11:2996-3001. [PMID: 27648475 DOI: 10.1021/acschembio.6b00565] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Drugs capable of trapping topoisomerase II (Top2), an essential enzyme that cleaves DNA to remove naturally occurring knots and tangles, can serve as potent anticancer agents. The monofunctional platinum agent phenanthriplatin, cis-[Pt(NH3)2(phenanthridine)Cl](NO3), is shown here to trap Top2 in addition to its known modes of inhibition of DNA and RNA polymerases. Its potency therefore combines diverse modes of action by which phenanthriplatin kills cancer cells. The observation that phenanthriplatin can act as a Top2 poison highlights opportunities to design nonclassical platinum anticancer agents with this novel mechanism of action. Such complexes have the potential to overcome current limitations with chemotherapy, such as resistance, and to provide treatment options for cancers that do not respond well to classical agents. Covalent DNA-platinum lesions implicated in Top2 poisoning are distinctive from those generated by known therapeutic topoisomerase poisons, which typically exert their action by reversible binding at the interface of Top2-DNA cleavage complexes.
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Affiliation(s)
- Imogen A. Riddell
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Keli Agama
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ga Young Park
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yves Pommier
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen J. Lippard
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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108
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Lopez-Mosqueda J, Maddi K, Prgomet S, Kalayil S, Marinovic-Terzic I, Terzic J, Dikic I. SPRTN is a mammalian DNA-binding metalloprotease that resolves DNA-protein crosslinks. eLife 2016; 5. [PMID: 27852435 PMCID: PMC5127644 DOI: 10.7554/elife.21491] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/15/2016] [Indexed: 01/22/2023] Open
Abstract
Ruijs-Aalfs syndrome is a segmental progeroid syndrome resulting from mutations in the SPRTN gene. Cells derived from patients with SPRTN mutations elicit genomic instability and people afflicted with this syndrome developed hepatocellular carcinoma. Here we describe the molecular mechanism by which SPRTN contributes to genome stability and normal cellular homeostasis. We show that SPRTN is a DNA-dependent mammalian protease required for resolving cytotoxic DNA-protein crosslinks (DPCs)— a function that had only been attributed to the metalloprotease Wss1 in budding yeast. We provide genetic evidence that SPRTN and Wss1 function distinctly in vivo to resolve DPCs. Upon DNA and ubiquitin binding, SPRTN can elicit proteolytic activity; cleaving DPC substrates and itself. SPRTN null cells or cells derived from patients with Ruijs-Aalfs syndrome are impaired in the resolution of covalent DPCs in vivo. Collectively, SPRTN is a mammalian protease required for resolving DNA-protein crosslinks in vivo whose function is compromised in Ruijs-Aalfs syndrome patients. DOI:http://dx.doi.org/10.7554/eLife.21491.001
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Affiliation(s)
- Jaime Lopez-Mosqueda
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Karthik Maddi
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Stefan Prgomet
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany
| | - Sissy Kalayil
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Ivana Marinovic-Terzic
- Department of Immunology and Medical Genetics, University of Split, School of Medicine, Split, Croatia
| | - Janos Terzic
- Department of Immunology and Medical Genetics, University of Split, School of Medicine, Split, Croatia
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
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109
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Rivalta I, Lisi GP, Snoeberger NS, Manley G, Loria JP, Batista VS. Allosteric Communication Disrupted by a Small Molecule Binding to the Imidazole Glycerol Phosphate Synthase Protein-Protein Interface. Biochemistry 2016; 55:6484-6494. [PMID: 27797506 DOI: 10.1021/acs.biochem.6b00859] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric enzymes regulate a wide range of catalytic transformations, including biosynthetic mechanisms of important human pathogens, upon binding of substrate molecules to an orthosteric (or active) site and effector ligands at distant (allosteric) sites. We find that enzymatic activity can be impaired by small molecules that bind along the allosteric pathway connecting the orthosteric and allosteric sites, without competing with endogenous ligands. Noncompetitive allosteric inhibitors disrupted allostery in the imidazole glycerol phosphate synthase (IGPS) enzyme from Thermotoga maritima as evidenced by nuclear magnetic resonance, microsecond time-scale molecular dynamics simulations, isothermal titration calorimetry, and kinetic assays. The findings are particularly relevant for the development of allosteric antibiotics, herbicides, and antifungal compounds because IGPS is absent in mammals but provides an entry point to fundamental biosynthetic pathways in plants, fungi, and bacteria.
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Affiliation(s)
- Ivan Rivalta
- Univ Lyon, ENS de Lyon, CNRS, Université Claude Bernard Lyon 1 , Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
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110
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Human Topoisomerase I mediated cytotoxicity profile of l-valine-quercetin diorganotin(IV) antitumor drug entities. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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111
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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112
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Takeda S, Hoa NN, Sasanuma H. The role of the Mre11-Rad50-Nbs1 complex in double-strand break repair-facts and myths. JOURNAL OF RADIATION RESEARCH 2016; 57 Suppl 1:i25-i32. [PMID: 27311583 PMCID: PMC4990115 DOI: 10.1093/jrr/rrw034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/16/2016] [Accepted: 02/23/2016] [Indexed: 06/06/2023]
Abstract
Homologous recombination (HR) initiates double-strand break (DSB) repair by digesting 5'-termini at DSBs, the biochemical reaction called DSB resection, during which DSBs are processed by nucleases to generate 3' single-strand DNA. Rad51 recombinase polymerizes along resected DNA, and the resulting Rad51-DNA complex undergoes homology search. Although DSB resection by the Mre11 nuclease plays a critical role in HR in Saccharomyces cerevisiae, it remains elusive whether DSB resection by Mre11 significantly contributes to HR-dependent DSB repair in mammalian cells. Depletion of Mre11 decreases the efficiency of DSB resection only by 2- to 3-fold in mammalian cells. We show that although Mre11 is required for efficient HR-dependent repair of ionizing-radiation-induced DSBs, Mre11 is largely dispensable for DSB resection in both chicken DT40 and human TK6 B cell lines. Moreover, a 2- to 3-fold decrease in DSB resection has virtually no impact on the efficiency of HR. Thus, although a large number of researchers have reported the vital role of Mre11-mediated DSB resection in HR, the role may not explain the very severe defect in HR in Mre11-deficient cells, including their lethality. We here show experimental evidence for the additional roles of Mre11 in (i) elimination of chemical adducts from DSB ends for subsequent DSB repair, and (ii) maintaining HR intermediates for their proper resolution.
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Affiliation(s)
- Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nguyen Ngoc Hoa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
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113
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Das SK, Rehman I, Ghosh A, Sengupta S, Majumdar P, Jana B, Das BB. Poly(ADP-ribose) polymers regulate DNA topoisomerase I (Top1) nuclear dynamics and camptothecin sensitivity in living cells. Nucleic Acids Res 2016; 44:8363-75. [PMID: 27466387 PMCID: PMC5041477 DOI: 10.1093/nar/gkw665] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/13/2016] [Indexed: 01/19/2023] Open
Abstract
Topoisomerase 1 (Top1) is essential for removing the DNA supercoiling generated during replication and transcription. Anticancer drugs like camptothecin (CPT) and its clinical derivatives exert their cytotoxicity by reversibly trapping Top1 in covalent complexes on the DNA (Top1cc). Poly(ADP-ribose) polymerase (PARP) catalyses the addition of ADP-ribose polymers (PAR) onto itself and Top1. PARP inhibitors enhance the cytotoxicity of CPT in the clinical trials. However, the molecular mechanism by which PARylation regulates Top1 nuclear dynamics is not fully understood. Using live-cell imaging of enhanced green fluorescence tagged-human Top1, we show that PARP inhibitors (Veliparib, ABT-888) delocalize Top1 from the nucleolus to the nucleoplasm, which is independent of Top1–PARP1 interaction. Using fluorescence recovery after photobleaching and subsequent fitting of the data employing kinetic modelling we demonstrate that ABT-888 markedly increase CPT-induced bound/immobile fraction of Top1 (Top1cc) across the nuclear genome, suggesting Top1-PARylation counteracts CPT-induced stabilization of Top1cc. We further show Trp205 and Asn722 of Top1 are critical for subnuclear dynamics. Top1 mutant (N722S) was restricted to the nucleolus in the presence of CPT due to its deficiency in the accumulation of CPT-induced Top1-PARylation and Top1cc formation. This work identifies ADP-ribose polymers as key determinant for regulating Top1 subnuclear dynamics.
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Affiliation(s)
- Subhendu K Das
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Ishita Rehman
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Arijit Ghosh
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Souvik Sengupta
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Papiya Majumdar
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Biman Jana
- Physical Chemistry Department, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Benu Brata Das
- Laboratory of Molecular Biology, Department of Physical Chemistry, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
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114
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Zhao XZ, Metifiot M, Smith SJ, Maddali K, Marchand C, Hughes SH, Pommier Y, Burke TR. 6,7-Dihydroxyisoindolin-1-one and 7,8-Dihydroxy-3,4-Dihydroisoquinolin- 1(2H)-one Based HIV-1 Integrase Inhibitors. Curr Top Med Chem 2016; 16:435-40. [PMID: 26268341 DOI: 10.2174/1568026615666150813150058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/22/2022]
Abstract
Integrase (IN) is an essential viral enzyme required for HIV-1 replication, which has been targeted by anti-AIDS therapeutics. Integrase strand transfer inhibitors (INSTIs) represent a new class of antiretroviral agents developed for the treatment of HIV-1 infections. Important structural features that are shared by many INSTIs include a coplanar arrangement of three heteroatoms that chelate two catalytic Mg(2+) ions in the IN active site and a linked halophenyl ring that binds in the hydrophobic pocket formed by the complex of IN with viral DNA. We recently reported bicyclic 6,7-dihydroxyoxoisoindolin-1-one-based IN inhibitors. In the current study, we modified these inhibitors in three ways. First, we increased the spacer length between the metalchelating triad and the halophenyl group. Second, we replaced the indoline [5,6] bicycle with a fused dihydroxyisoquinolinones [6,6] ring system. Finally, we prepared bis-6,7-dihydroxyisoindolin-1-one-4-sulfonamides as dimeric HIV-1 IN inhibitors. These new analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA.
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115
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Métifiot M, Johnson BC, Kiselev E, Marler L, Zhao XZ, Burke TR, Marchand C, Hughes SH, Pommier Y. Selectivity for strand-transfer over 3'-processing and susceptibility to clinical resistance of HIV-1 integrase inhibitors are driven by key enzyme-DNA interactions in the active site. Nucleic Acids Res 2016; 44:6896-906. [PMID: 27369381 PMCID: PMC5001616 DOI: 10.1093/nar/gkw592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 06/21/2016] [Indexed: 12/23/2022] Open
Abstract
Integrase strand transfer inhibitors (INSTIs) are highly effective against HIV infections. Co-crystal structures of the prototype foamy virus intasome have shown that all three FDA-approved drugs, raltegravir (RAL), elvitegravir and dolutegravir (DTG), act as interfacial inhibitors during the strand transfer (ST) integration step. However, these structures give only a partial sense for the limited inhibition of the 3′-processing reaction by INSTIs and how INSTIs can be modified to overcome drug resistance, notably against the G140S-Q148H double mutation. Based on biochemical experiments with modified oligonucleotides, we demonstrate that both the viral DNA +1 and −1 bases, which flank the 3′-processing site, play a critical role for 3′-processing efficiency and inhibition by RAL and DTG. In addition, the G140S-Q148H (SH) mutant integrase, which has a reduced 3′-processing activity, becomes more active and more resistant to inhibition of 3′-processing by RAL and DTG in the absence of the −1 and +1 bases. Molecular modeling of HIV-1 integrase, together with biochemical data, indicate that the conserved residue Q146 in the flexible loop of HIV-1 integrase is critical for productive viral DNA binding through specific contacts with the virus DNA ends in the 3′-processing and ST reactions. The potency of integrase inhibitors against 3′-processing and their ability to overcome resistance is discussed.
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Affiliation(s)
- Mathieu Métifiot
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Barry C Johnson
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Laura Marler
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Center for Cancer Research, National Institutes of Health, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
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116
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Iwasaki S, Floor SN, Ingolia NT. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature 2016; 534:558-61. [PMID: 27309803 PMCID: PMC4946961 DOI: 10.1038/nature17978] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 04/05/2016] [Indexed: 02/07/2023]
Abstract
Rocaglamide A (RocA) typifies a class of protein synthesis inhibitors that selectively kill aneuploid tumor cells and repress translation of specific mRNAs1-4. RocA targets eukaryotic initiation factor 4A (eIF4A), an ATP-dependent DEAD-box RNA helicase; its mRNA selectivity is proposed to reflect highly structured 5′ UTRs that depend strongly on eIF4A-mediated unwinding5. However, rocaglate treatment may not phenocopy the loss of eIF4A activity, as these drugs actually increase the affinity between eIF4A and RNA1,2,6. Here, we show that secondary structure in 5′ UTRs is only a minor determinant for RocA selectivity and RocA does not repress translation by reducing eIF4A availability. Rather, in vitro and in cells, RocA specifically clamps eIF4A onto polypurine sequences in an ATP-independent manner. This artificially clamped eIF4A blocks 43S scanning, leading to premature, upstream translation initiation and reducing protein expression from transcripts bearing the RocA-eIF4A target sequence. In elucidating the mechanism of selective translation repression by this lead anti-cancer compound, we provide an example of a drug stabilizing sequence-selective RNA-protein interactions.
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Affiliation(s)
- Shintaro Iwasaki
- Department of Molecular and Cell Biology, Center for RNA Systems Biology, University of California, Berkeley, California 94720, USA
| | - Stephen N Floor
- Department of Molecular and Cell Biology, Center for RNA Systems Biology, University of California, Berkeley, California 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, Center for RNA Systems Biology, University of California, Berkeley, California 94720, USA
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117
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Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR. HIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases. ACS Chem Biol 2016; 11:1074-81. [PMID: 26808478 PMCID: PMC4836387 DOI: 10.1021/acschembio.5b00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
HIV
integrase (IN) strand transfer inhibitors (INSTIs) are among
the newest anti-AIDS drugs; however, mutant forms of IN can confer
resistance. We developed noncytotoxic naphthyridine-containing INSTIs
that retain low nanomolar IC50 values against HIV-1 variants
harboring all of the major INSTI-resistant mutations. We found by
analyzing crystal structures of inhibitors bound to the IN from the
prototype foamy virus (PFV) that the most successful inhibitors show
striking mimicry of the bound viral DNA prior to 3′-processing
and the bound host DNA prior to strand transfer. Using this concept
of “bi-substrate mimicry,” we developed a new broadly
effective inhibitor that not only mimics aspects of both the bound
target and viral DNA but also more completely fills the space they
would normally occupy. Maximizing shape complementarity and recapitulating
structural components encompassing both of the IN DNA substrates could
serve as a guiding principle for the development of new INSTIs.
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Affiliation(s)
| | | | - Daniel P. Maskell
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
| | - Mathieu Metifiot
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Valerie E. Pye
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
| | - Katherine Fesen
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christophe Marchand
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yves Pommier
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Peter Cherepanov
- Clare
Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, EN6 3LD, United Kingdom
- Imperial College London, St-Mary’s
Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Stephen H. Hughes
- Developmental
Therapeutics Branch and Laboratory of Molecular Pharmacology, Center
for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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118
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Vann KR, Ekiz G, Zencir S, Bedir E, Topcu Z, Osheroff N. Effects of Secondary Metabolites from the Fungus Septofusidium berolinense on DNA Cleavage Mediated by Human Topoisomerase IIα. Chem Res Toxicol 2016; 29:415-20. [PMID: 26894873 DOI: 10.1021/acs.chemrestox.6b00009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two metabolites from the ascomycete fungus Septofusidium berolinense were recently identified as having antineoplastic activity [Ekiz et al. (2015) J. Antibiot. , DOI: 10.1038/ja.2015.84]. However, the basis for this activity is not known. One of the compounds [3,6-dihydroxy-2-propylbenzaldehyde (GE-1)] is a hydroquinone, and the other [2-hydroxymethyl-3-propylcyclohexa-2,5-diene-1,4-dione (GE-2)] is a quinone. Because some hydroquinones and quinones act as topoisomerase II poisons, the effects of GE-1 and GE-2 on DNA cleavage mediated by human topoisomerase IIα were assessed. GE-2 enhanced DNA cleavage ∼4-fold and induced scission with a site specificity similar to that of the anticancer drug etoposide. Similar to other quinone-based topoisomerase II poisons, GE-2 displayed several hallmark characteristics of covalent topoisomerase II poisons, including (1) the inability to poison a topoisomerase IIα construct that lacks the N-terminal domain, (2) the inhibition of DNA cleavage when the compound was incubated with the enzyme prior to the addition of plasmid, and (3) the loss of poisoning activity in the presence of a reducing agent. In contrast to GE-2, GE-1 did not enhance DNA cleavage mediated by topoisomerase IIα except at very high concentrations. However, the activity and potency of the metabolite were dramatically enhanced under oxidizing conditions. These results suggest that topoisomerase IIα may play a role in mediating the cytotoxic effects of these fungal metabolites.
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Affiliation(s)
| | | | - Sevil Zencir
- Department of Medical Biology, Faculty of Medicine, Pamukkale University , 20070 Denizli, Turkey
| | | | | | - Neil Osheroff
- VA Tennessee Valley Healthcare System , Nashville, Tennessee 37212, United States
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119
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Jeszenői N, Bálint M, Horváth I, van der Spoel D, Hetényi C. Exploration of Interfacial Hydration Networks of Target–Ligand Complexes. J Chem Inf Model 2016; 56:148-58. [DOI: 10.1021/acs.jcim.5b00638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Norbert Jeszenői
- Department
of Genetics, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
- MTA
NAP-B Molecular Neuroendocrinology Group, Institute of Physiology,
Szentágothai Research Center, Center for Neuroscience, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Mónika Bálint
- Department
of Biochemistry, Eötvös Loránd University, Pázmány
Péter sétány 1/C, 1117 Budapest, Hungary
| | - István Horváth
- Chemistry
Doctoral School, University of Szeged, Dugonics tér 13, 6720 Szeged, Hungary
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, University of Uppsala, Box 596, SE-75124 Uppsala, Sweden
| | - Csaba Hetényi
- MTA-ELTE
Molecular Biophysics Research Group, Hungarian Academy of Sciences, Pázmány sétány 1/C, 1117 Budapest, Hungary
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120
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Hasinoff BB, Wu X, Patel D, Kanagasabai R, Karmahapatra S, Yalowich JC. Mechanisms of Action and Reduced Cardiotoxicity of Pixantrone; a Topoisomerase II Targeting Agent with Cellular Selectivity for the Topoisomerase IIα Isoform. J Pharmacol Exp Ther 2015; 356:397-409. [PMID: 26660439 DOI: 10.1124/jpet.115.228650] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/09/2015] [Indexed: 01/09/2023] Open
Abstract
Pixantrone is a new noncardiotoxic aza-anthracenedione anticancer drug structurally related to anthracyclines and anthracenediones, such as doxorubicin and mitoxantrone. Pixantrone is approved in the European Union for the treatment of relapsed or refractory aggressive B cell non-Hodgkin lymphoma. This study was undertaken to investigate both the mechanism(s) of its anticancer activity and its relative lack of cardiotoxicity. Pixantrone targeted DNA topoisomerase IIα as evidenced by its ability to inhibit kinetoplast DNA decatenation; to produce linear double-strand DNA in a pBR322 DNA cleavage assay; to produce DNA double-strand breaks in a cellular phospho-histone γH2AX assay; to form covalent topoisomerase II-DNA complexes in a cellular immunodetection of complex of enzyme-to-DNA assay; and to display cross-resistance in etoposide-resistant K562 cells. Pixantrone produced semiquinone free radicals in an enzymatic reducing system, although not in a cellular system, most likely due to low cellular uptake. Pixantrone was 10- to 12-fold less damaging to neonatal rat myocytes than doxorubicin or mitoxantrone, as measured by lactate dehydrogenase release. Three factors potentially contribute to the reduced cardiotoxicity of pixantrone. First, its lack of binding to iron(III) makes it unable to induce iron-based oxidative stress. Second, its low cellular uptake may limit its ability to produce semiquinone free radicals and redox cycle. Finally, because the β isoform of topoisomerase II predominates in postmitotic cardiomyocytes, and pixantrone is demonstrated in this study to be selective for topoisomerase IIα in stabilizing enzyme-DNA covalent complexes, the attenuated cardiotoxicity of this agent may also be due to its selectivity for targeting topoisomerase IIα over topoisomerase IIβ.
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Affiliation(s)
- Brian B Hasinoff
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
| | - Xing Wu
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
| | - Daywin Patel
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
| | - Ragu Kanagasabai
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
| | - Soumendrakrishna Karmahapatra
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
| | - Jack C Yalowich
- College of Pharmacy, Apotex Centre, University of Manitoba, Winnipeg, Manitoba, Canada (B.B.H., X.W., D.P.); and Division of Pharmacology, College of Pharmacy, Ohio State University, Columbus, Ohio (R.K., S.K., J.C.Y.)
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121
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Byun JS, Sohn JM, Leem DG, Park B, Nam JH, Shin DH, Shin JS, Kim HJ, Lee KT, Lee JY. In vitro synergistic anticancer activity of the combination of T-type calcium channel blocker and chemotherapeutic agent in A549 cells. Bioorg Med Chem Lett 2015; 26:1073-1079. [PMID: 26739776 DOI: 10.1016/j.bmcl.2015.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 11/10/2015] [Accepted: 12/04/2015] [Indexed: 01/15/2023]
Abstract
As a result of our continuous research, new 3,4-dihydroquinazoline derivative containing ureido group, KCP10043F was synthesized and evaluated for T-type Ca(2+) channel (Cav3.1) blockade, cytotoxicity, and cell cycle arrest against human non-small cell lung (A549) cells. KCP10043F showed both weaker T-type Ca(2+) channel blocking activity and less cytotoxicity against A549 cells than parent compound KYS05090S [4-(benzylcarbamoylmethyl)-3-(4-biphenylyl)-2-(N,N',N'-trimethyl-1,5-pentanediamino)-3,4-dihydroquinazoline 2 hydrochloride], but it exhibited more potent G1-phase arrest than KYS05090S in A549 cells. This was found to be accompanied by the downregulations of cyclin-dependent kinase (CDK) 2, CDK4, CDK6, cyclin D2, cyclin D3, and cyclin E at the protein levels. However, p27(KIP1) as a CDK inhibitor was gradually upregulated at the protein levels and increased recruitment to CDK2, CDK4 and CDK6 after KCP10043F treatment. Based on the strong G1-phase cell cycle arrest of KCP10043F in A549 cells, the combination of KCP10043F with etoposide (or cisplatin) resulted in a synergistic cell death (combination index=0.2-0.8) via the induction of apoptosis compared with either agent alone. Taken together with these overall results and the favorable in vitro ADME (absorption, distribution, metabolism, and excretion) profiles of KCP10043F, therefore, it could be used as a potential agent for the combination therapy on human lung cancer.
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Affiliation(s)
- Joon Seok Byun
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Joo Mi Sohn
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Dong Gyu Leem
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Byeongyeon Park
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Ji Hye Nam
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Dong Hyun Shin
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Ji Sun Shin
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Hyoung Ja Kim
- Molecular Recognition Research Center, Future Convergence Research Division, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Kyung-Tae Lee
- Department of Life and Nanopharmaceutical Science, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
| | - Jae Yeol Lee
- Research Institute for Basic Sciences and Department of Chemistry, College of Sciences, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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122
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Schovanek J, Bullova P, Tayem Y, Giubellino A, Wesley R, Lendvai N, Nölting S, Kopacek J, Frysak Z, Pommier Y, Kummar S, Pacak K. Inhibitory Effect of the Noncamptothecin Topoisomerase I Inhibitor LMP-400 on Female Mice Models and Human Pheochromocytoma Cells. Endocrinology 2015; 156:4094-104. [PMID: 26267380 PMCID: PMC4606751 DOI: 10.1210/en.2015-1476] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Metastatic pheochromocytoma continues to be an incurable disease, and treatment with conventional cytotoxic chemotherapy offers limited efficacy. In the present study, we evaluated a novel topoisomerase I inhibitor, LMP-400, as a potential treatment for this devastating disease. We found a high expression of topoisomerase I in human metastatic pheochromocytoma, providing a basis for the evaluation of a topoisomerase 1 inhibitor as a therapeutic strategy. LMP-400 inhibited the cell growth of established mouse pheochromocytoma cell lines and primary human tumor tissue cultures. In a study performed in athymic female mice, LMP-400 demonstrated a significant inhibitory effect on tumor growth with two drug administration regimens. Furthermore, low doses of LMP-400 decreased the protein levels of hypoxia-inducible factor 1 (HIF-1α), one of a family of factors studied as potential metastatic drivers in these tumors. The HIF-1α decrease resulted in changes in the mRNA levels of HIF-1 transcriptional targets. In vitro, LMP-400 showed an increase in the growth-inhibitory effects in combination with other chemotherapeutic drugs that are currently used for the treatment of pheochromocytoma. We conclude that LMP-400 has promising antitumor activity in preclinical models of metastatic pheochromocytoma and its use should be considered in future clinical trials.
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MESH Headings
- Adrenal Gland Neoplasms/drug therapy
- Adrenal Gland Neoplasms/enzymology
- Adrenal Gland Neoplasms/pathology
- Animals
- Antineoplastic Agents/pharmacology
- Benzodioxoles/administration & dosage
- Benzodioxoles/pharmacology
- Blotting, Western
- Cell Hypoxia
- Cell Line, Tumor
- Cell Proliferation/drug effects
- DNA Topoisomerases, Type I/metabolism
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Drug Synergism
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Isoquinolines/administration & dosage
- Isoquinolines/pharmacology
- Liver Neoplasms/drug therapy
- Liver Neoplasms/enzymology
- Liver Neoplasms/secondary
- Lung Neoplasms/drug therapy
- Lung Neoplasms/enzymology
- Lung Neoplasms/secondary
- Mice, Nude
- PC12 Cells
- Pheochromocytoma/drug therapy
- Pheochromocytoma/enzymology
- Pheochromocytoma/pathology
- Rats
- Reverse Transcriptase Polymerase Chain Reaction
- Topoisomerase I Inhibitors/administration & dosage
- Topoisomerase I Inhibitors/pharmacology
- Tumor Cells, Cultured
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Affiliation(s)
- Jan Schovanek
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Petra Bullova
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Yasin Tayem
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Alessio Giubellino
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Robert Wesley
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Nikoletta Lendvai
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Svenja Nölting
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Juraj Kopacek
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Zdenek Frysak
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Yves Pommier
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Shivaani Kummar
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
| | - Karel Pacak
- Program in Reproductive and Adult Endocrinology (J.S., P.B., Y.T., A.G., N.L., S.N., K.P.), Eunice Kennedy Shriver National Institute of Child Health and Human Development, Warren G. Magnuson Clinical Center (R.W.), and National Cancer Institute (Y.P., S.K.), National Institutes of Health, Bethesda, Maryland 20892-1109; Department of Internal Medicine III-Nephrology, Rheumatology, and Endocrinology (J.S., Z.F.), Faculty of Medicine and Dentistry, Palacky University, 771 47 Olomouc, Czech Republic; Department of Molecular Medicine (P.B., J.K.), Institute of Virology, Slovak Academy of Sciences, 845 05 Bratislava, Slovak Republic; and Department of Internal Medicine II (S.N.), Campus Grosshadern, University-Hospital of the Ludwig-Maximilians-University of Munich, 80539 Munich, Germany
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Seol Y, Zhang H, Agama K, Lorence N, Pommier Y, Neuman KC. Single-Molecule Supercoil Relaxation Assay as a Screening Tool to Determine the Mechanism and Efficacy of Human Topoisomerase IB Inhibitors. Mol Cancer Ther 2015; 14:2552-9. [PMID: 26351326 PMCID: PMC4636450 DOI: 10.1158/1535-7163.mct-15-0454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/27/2015] [Indexed: 11/16/2022]
Abstract
Human nuclear type IB topoisomerase (Top1) inhibitors are widely used and powerful anticancer agents. In this study, we introduce and validate a single-molecule supercoil relaxation assay as a molecular pharmacology tool for characterizing therapeutically relevant Top1 inhibitors. Using this assay, we determined the effects on Top1 supercoil relaxation activity of four Top1 inhibitors; three clinically relevant: camptothecin, LMP-400, LMP-776 (both indenoisoquinoline derivatives), and one natural product in preclinical development, lamellarin-D. Our results demonstrate that Top1 inhibitors have two distinct effects on Top1 activity: a decrease in supercoil relaxation rate and an increase in religation inhibition. The type and magnitude of the inhibition mode depend both on the specific inhibitor and on the topology of the DNA substrate. In general, the efficacy of inhibition is significantly higher with supercoiled than with relaxed DNA substrates. Comparing single-molecule inhibition with cell growth inhibition (IC50) measurements showed a correlation between the binding time of the Top1 inhibitors and their cytotoxic efficacy, independent of the mode of inhibition. This study demonstrates that the single-molecule supercoil relaxation assay is a sensitive method to elucidate the detailed mechanisms of Top1 inhibitors and is relevant for the cellular efficacy of Top1 inhibitors.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nicholas Lorence
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland.
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Hou Q, Dutilh BE, Huynen MA, Heringa J, Feenstra KA. Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case. BMC Bioinformatics 2015; 16:325. [PMID: 26449222 PMCID: PMC4599308 DOI: 10.1186/s12859-015-0758-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/30/2015] [Indexed: 11/17/2022] Open
Abstract
Background Protein families participating in protein-protein interactions may contain sub-families that have different binding characteristics, ranging from right binding to showing no interaction at all. Composition differences at the sequence level in these sub-families are often decisive to their differential functional interaction. Methods to predict interface sites from protein sequences typically exploit conservation as a signal. Here, instead, we provide proof of concept that the sequence specificity between interacting versus non-interacting groups can be exploited to recognise interaction sites. Results We collected homodimeric and monomeric proteins and formed homologous groups, each having an interacting (homodimer) subgroup and a non-interacting (monomer) subgroup. We then compiled multiple sequence alignments of the proteins in the homologous groups and identified compositional differences between the homodimeric and monomeric subgroups for each of the alignment positions. Our results show that this specificity signal distinguishes interface and other surface residues with 40.9 % recall and up to 25.1 % precision. Conclusions To our best knowledge, this is the first large scale study that exploits sequence specificity between interacting and non-interacting homologs to predict interaction sites from sequence information only. The performance obtained indicates that this signal contains valuable information to identify protein-protein interaction sites. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0758-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qingzhen Hou
- Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands. .,Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
| | - Jaap Heringa
- Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.
| | - K Anton Feenstra
- Center for Integrative Bioinformatics VU (IBIVU), Vrije University Amsterdam, De Boelelaan 1081A, 1081 HV, Amsterdam, The Netherlands.
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Grandgenett DP, Pandey KK, Bera S, Aihara H. Multifunctional facets of retrovirus integrase. World J Biol Chem 2015; 6:83-94. [PMID: 26322168 PMCID: PMC4549773 DOI: 10.4331/wjbc.v6.i3.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/01/2015] [Accepted: 07/27/2015] [Indexed: 02/05/2023] Open
Abstract
The retrovirus integrase (IN) is responsible for integration of the reverse transcribed linear cDNA into the host DNA genome. First, IN cleaves a dinucleotide from the 3’ OH blunt ends of the viral DNA exposing the highly conserved CA sequence in the recessed ends. IN utilizes the 3’ OH ends to catalyze the concerted integration of the two ends into opposite strands of the cellular DNA producing 4 to 6 bp staggered insertions, depending on the retrovirus species. The staggered ends are repaired by host cell machinery that results in a permanent copy of the viral DNA in the cellular genome. Besides integration, IN performs other functions in the replication cycle of several studied retroviruses. The proper organization of IN within the viral internal core is essential for the correct maturation of the virus. IN plays a major role in reverse transcription by interacting directly with the reverse transcriptase and by binding to the viral capsid protein and a cellular protein. Recruitment of several other host proteins into the viral particle are also promoted by IN. IN assists with the nuclear transport of the preintegration complex across the nuclear membrane. With several retroviruses, IN specifically interacts with different host protein factors that guide the preintegration complex to preferentially integrate the viral genome into specific regions of the host chromosomal target. Human gene therapy using retrovirus vectors is directly affected by the interactions of IN with these host factors. Inhibitors directed against the human immunodeficiency virus (HIV) IN bind within the active site of IN containing viral DNA ends thus preventing integration and subsequent HIV/AIDS.
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Vann KR, Sedgeman CA, Gopas J, Golan-Goldhirsh A, Osheroff N. Effects of Olive Metabolites on DNA Cleavage Mediated by Human Type II Topoisomerases. Biochemistry 2015; 54:4531-41. [PMID: 26132160 PMCID: PMC4520624 DOI: 10.1021/acs.biochem.5b00162] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Several
naturally occurring dietary polyphenols with chemopreventive
or anticancer properties are topoisomerase II poisons. To identify
additional phytochemicals that enhance topoisomerase II-mediated DNA
cleavage, a library of 341 Mediterranean plant extracts was screened
for activity against human topoisomerase IIα. An extract from Phillyrea latifolia L., a member of the olive tree family,
displayed high activity against the human enzyme. On the basis of
previous metabolomics studies, we identified several polyphenols (hydroxytyrosol,
oleuropein, verbascoside, tyrosol, and caffeic acid) as potential
candidates for topoisomerase II poisons. Of these, hydroxytyrosol,
oleuropein, and verbascoside enhanced topoisomerase II-mediated DNA
cleavage. The potency of these olive metabolites increased 10–100-fold
in the presence of an oxidant. Hydroxytyrosol, oleuropein, and verbascoside
displayed hallmark characteristics of covalent topoisomerase II poisons.
(1) The activity of the metabolites was abrogated by a reducing agent.
(2) Compounds inhibited topoisomerase II activity when they were incubated
with the enzyme prior to the addition of DNA. (3) Compounds were unable
to poison a topoisomerase IIα construct that lacked the N-terminal
domain. Because hydroxytyrosol, oleuropein, and verbascoside are broadly
distributed across the olive family, extracts from the leaves, bark,
and fruit of 11 olive tree species were tested for activity against
human topoisomerase IIα. Several of the extracts enhanced enzyme-mediated
DNA cleavage. Finally, a commercial olive leaf supplement and extra
virgin olive oils pressed from a variety of Olea europea subspecies enhanced DNA cleavage mediated by topoisomerase IIα.
Thus, olive metabolites appear to act as topoisomerase II poisons
in complex formulations intended for human dietary consumption.
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Affiliation(s)
| | | | - Jacob Gopas
- ∥Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,⊥Department of Oncology, Soroka University Medical Center, Beer Sheva 84105, Israel
| | - Avi Golan-Goldhirsh
- @The Jacob Blaustein Institutes for Desert Research (BIDR), French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Sede Boqer Campus, Beer Sheva 84990, Israel
| | - Neil Osheroff
- §VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. CHEMISTRY & BIOLOGY 2015; 22:689-703. [PMID: 26091166 PMCID: PMC4518475 DOI: 10.1016/j.chembiol.2015.04.019] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/01/2015] [Accepted: 04/08/2015] [Indexed: 01/19/2023]
Abstract
Protein-protein interactions (PPIs) underlie the majority of biological processes, signaling, and disease. Approaches to modulate PPIs with small molecules have therefore attracted increasing interest over the past decade. However, there are a number of challenges inherent in developing small-molecule PPI inhibitors that have prevented these approaches from reaching their full potential. From target validation to small-molecule screening and lead optimization, identifying therapeutically relevant PPIs that can be successfully modulated by small molecules is not a simple task. Following the recent review by Arkin et al., which summarized the lessons learnt from prior successes, we focus in this article on the specific challenges of developing PPI inhibitors and detail the recent advances in chemistry, biology, and computation that facilitate overcoming them. We conclude by providing a perspective on the field and outlining four innovations that we see as key enabling steps for successful development of small-molecule inhibitors targeting PPIs.
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Affiliation(s)
- Luca Laraia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - Grahame McKenzie
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
| | - David J Huggins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK.
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Activation of RAF1 (c-RAF) by the Marine Alkaloid Lasonolide A Induces Rapid Premature Chromosome Condensation. Mar Drugs 2015; 13:3625-39. [PMID: 26058013 PMCID: PMC4483648 DOI: 10.3390/md13063625] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 01/12/2023] Open
Abstract
Lasonolide A (LSA), a potent antitumor polyketide from the marine sponge, Forcepia sp., induces rapid and reversible protein hyperphosphorylation and premature chromosome condensation (PCC) at nanomolar concentrations independent of cyclin-dependent kinases. To identify cellular targets of LSA, we screened 2951 shRNAs targeting a pool of human kinases and phosphatases (1140 RefSeqs) to identify genes that modulate PCC in response to LSA. This led to the identification of RAF1 (C-RAF) as a mediator of LSA-induced PCC, as shRNAs against RAF1 conferred resistance to LSA. We found that LSA induced RAF1 phosphorylation on Serine 338 within minutes in human colorectal carcinoma HCT-116, ovarian carcinoma OVCAR-8, and Burkitt’s lymphoma CA46 cell lines. RAF1 depletion by siRNAs attenuated LSA-induced PCC in HCT-116 and OVCAR-8 cells. Furthermore, mouse embryonic fibroblasts (MEF) with homozygous deletion in Raf1, but not deletion in the related kinase Braf, were resistant to LSA-induced PCC. Complementation of Raf1−/− MEFs with wild-type human RAF1, but not with kinase-dead RAF1 mutant, restored LSA-induced PCC. Finally, the Raf inhibitor sorafenib, but not the MEK inhibitor AZD6244, effectively suppressed LSA-induced PCC. Our findings implicate a previously unknown, MAPK-independent role of RAF1 in chromatin condensation and potent activation of this pathway by LSA.
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Kellermann G, Kaiser M, Dingli F, Lahuna O, Naud-Martin D, Mahuteau-Betzer F, Loew D, Ségal-Bendirdjian E, Teulade-Fichou MP, Bombard S. Identification of human telomerase assembly inhibitors enabled by a novel method to produce hTERT. Nucleic Acids Res 2015; 43:e99. [PMID: 25958399 PMCID: PMC4551907 DOI: 10.1093/nar/gkv425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/20/2015] [Indexed: 01/23/2023] Open
Abstract
Telomerase is the enzyme that maintains the length of telomeres. It is minimally constituted of two components: a core reverse transcriptase protein (hTERT) and an RNA (hTR). Despite its significance as an almost universal cancer target, the understanding of the structure of telomerase and the optimization of specific inhibitors have been hampered by the limited amount of enzyme available. Here, we present a breakthrough method to produce unprecedented amounts of recombinant hTERT and to reconstitute human telomerase with purified components. This system provides a decisive tool to identify regulators of the assembly of this ribonucleoprotein complex. It also enables the large-scale screening of small-molecules capable to interfere with telomerase assembly. Indeed, it has allowed us to identify a compound that inhibits telomerase activity when added prior to the assembly of the enzyme, while it has no effect on an already assembled telomerase. Therefore, the novel system presented here may accelerate the understanding of human telomerase assembly and facilitate the discovery of potent and mechanistically unique inhibitors.
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Affiliation(s)
- Guillaume Kellermann
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
| | - Markus Kaiser
- Institut Curie, CMIB, CNRS UMR 9187- INSERM U1196, Orsay, France
| | - Florent Dingli
- Institut Curie/laboratoire de spectrométrie de masse protéomique, Paris, France
| | | | | | | | - Damarys Loew
- Institut Curie/laboratoire de spectrométrie de masse protéomique, Paris, France
| | - Evelyne Ségal-Bendirdjian
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
| | | | - Sophie Bombard
- INSERM UMR-S 1007, Cellular Homeostasis and Cancer, Paris, France Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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Abstract
The mammalian CtIP protein and its orthologs in other eukaryotes promote the resection of DNA double-strand breaks and are essential for meiotic recombination. Here we review the current literature supporting the role of CtIP in DNA end processing and the importance of CtIP endonuclease activity in DNA repair. We also examine the regulation of CtIP function by post-translational modifications, and its involvement in transcription- and replication-dependent functions through association with other protein complexes. The tumor suppressor function of CtIP likely is dependent on a combination of these roles in many aspects of DNA metabolism.
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131
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Beck DE, Abdelmalak M, Lv W, Reddy PVN, Tender GS, O'Neill E, Agama K, Marchand C, Pommier Y, Cushman M. Discovery of potent indenoisoquinoline topoisomerase I poisons lacking the 3-nitro toxicophore. J Med Chem 2015; 58:3997-4015. [PMID: 25909279 DOI: 10.1021/acs.jmedchem.5b00303] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
3-Nitroindenoisoquinoline human topoisomerase IB (Top1) poisons have potent antiproliferative effects on cancer cells. The undesirable nitro toxicophore could hypothetically be replaced by other functional groups that would retain the desired biological activities and minimize potential safety risks. Eleven series of indenoisoquinolines bearing 3-nitro bioisosteres were synthesized. The molecules were evaluated in the Top1-mediated DNA cleavage assay and in the National Cancer Institute's 60 cell line cytotoxicity assay. The data reveal that fluorine and chlorine may substitute for the 3-nitro group with minimal loss of Top1 poisoning activity. The new information gained from these efforts can be used to design novel indenoisoquinolines with improved safety.
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Affiliation(s)
- Daniel E Beck
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Monica Abdelmalak
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Wei Lv
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - P V Narasimha Reddy
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Gabrielle S Tender
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Elizaveta O'Neill
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Keli Agama
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Christophe Marchand
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Yves Pommier
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Mark Cushman
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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Structure-based design, synthesis and biological testing of piperazine-linked bis-epipodophyllotoxin etoposide analogs. Bioorg Med Chem 2015; 23:3542-51. [PMID: 25922181 DOI: 10.1016/j.bmc.2015.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/01/2015] [Accepted: 04/09/2015] [Indexed: 11/20/2022]
Abstract
Drugs that target DNA topoisomerase II, such as the epipodophyllotoxin etoposide, are a clinically important class of anticancer agents. A recently published X-ray structure of a ternary complex of etoposide, cleaved DNA and topoisomerase IIβ showed that the two intercalated etoposide molecules in the complex were separated by four DNA base pairs. Thus, using a structure-based design approach, a series of bis-epipodophyllotoxin etoposide analogs with piperazine-containing linkers was designed to simultaneously bind to these two sites. It was hypothesized that two-site binding would produce a more stable cleavage complex, and a more potent anticancer drug. The most potent bis-epipodophyllotoxin, which was 10-fold more growth inhibitory toward human erythroleukemic K562 cells than etoposide, contained a linker with eight methylene groups. All of the mono- and bis-epipodophyllotoxins, in a variety of assays, showed strong evidence that they targeted topoisomerase II. COMPARE analysis of NCI 60-cell GI50 endpoint data was also consistent with these compounds targeting topoisomerase II.
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Gold nanostar based biosensor detects epigenetic alterations on promoter of real cells. Biosens Bioelectron 2015; 66:497-503. [DOI: 10.1016/j.bios.2014.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 11/18/2022]
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Shen Y, Aoyagi-Scharber M, Wang B. Trapping Poly(ADP-Ribose) Polymerase. J Pharmacol Exp Ther 2015; 353:446-57. [DOI: 10.1124/jpet.114.222448] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/09/2015] [Indexed: 12/16/2022] Open
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Ashour ME, Atteya R, El-Khamisy SF. Topoisomerase-mediated chromosomal break repair: an emerging player in many games. Nat Rev Cancer 2015; 15:137-51. [PMID: 25693836 DOI: 10.1038/nrc3892] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mammalian genome is constantly challenged by exogenous and endogenous threats. Although much is known about the mechanisms that maintain DNA and RNA integrity, we know surprisingly little about the mechanisms that underpin the pathology and tissue specificity of many disorders caused by defective responses to DNA or RNA damage. Of the different types of endogenous damage, protein-linked DNA breaks (PDBs) are emerging as an important player in cancer development and therapy. PDBs can arise during the abortive activity of DNA topoisomerases, a class of enzymes that modulate DNA topology during several chromosomal transactions, such as gene transcription and DNA replication, recombination and repair. In this Review, we discuss the mechanisms underpinning topoisomerase-induced PDB formation and repair with a focus on their role during gene transcription and the development of tissue-specific cancers.
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Affiliation(s)
- Mohamed E Ashour
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Sherif F El-Khamisy
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
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136
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Li J, Ouyang Y, Zhang X, Zhou W, Wang F, Huang Z, Wang X, Chen Y, Zhang H, Fu L. Effect of HM910, a novel camptothecin derivative, on the inhibition of multiple myeloma cell growth in vitro and in vivo. Am J Cancer Res 2015; 5:1000-1016. [PMID: 26045982 PMCID: PMC4449431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023] Open
Abstract
Despite a variety of novel therapeutic agents, such as bortezomib, thalidomide and topotecan, multiple myeloma (MM) remains an incurable disease, thus the development of new chemotherapeutical agents is of high priority. We found HM910, a novel camptothecin (CPT) derivative, exhibited potent inhibition of MM cell growth in vitro and in xenografts of nude mice. Mechanistically, HM910 reduced the mitochondrial transmembrane potential (ΔΨm) via an increase in reactive oxygen species (ROS), which eventually resulting in the release of cytochrome c and the activation of mitochondrial-dependent apoptotic pathway. On the other hand, HM910 significantly triggered cell cycle arrest in G1 phase via downregulating the expressions of cyclin dependent kinase (CDK) 4 and 6, resulting in down-regulation of cyclin D1. Therefore, HM910 maybe a promising candidate for treating MM patients and is currently in phase I clinical trial in China.
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Affiliation(s)
- Juan Li
- First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, China
| | - Yudan Ouyang
- First Affiliated Hospital, Sun Yat-sen UniversityGuangzhou 510080, China
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Xu Zhang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Wenqiang Zhou
- Fangsheng Pharmaceuticals, IncChangsha 410000, China
| | - Fang Wang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Zhencong Huang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Xiaokun Wang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Yifan Chen
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Hui Zhang
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine; Cancer Center, Sun Yat-sen UniversityGuangzhou 510060, China
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137
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Small molecules, peptides and natural products: getting a grip on 14-3-3 protein-protein modulation. Future Med Chem 2015; 6:903-21. [PMID: 24962282 DOI: 10.4155/fmc.14.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
One of the proteins that is found in a diverse range of eukaryotic protein-protein interactions is the adaptor protein 14-3-3. As 14-3-3 is a hub protein with very diverse interactions, it is a good model to study various protein-protein interactions. A wide range of classes of molecules, peptides, small molecules or natural products, has been used to modify the protein interactions, providing both stabilization or inhibition of the interactions of 14-3-3 with its binding partners. The first protein crystal structures were solved in 1995 and gave molecular insights for further research. The plant analog of 14-3-3 binds to a plant plasma membrane H(+)-ATPase and this protein complex is stabilized by the fungal phytotoxin fusicoccin A. The knowledge gained from the process in plants was transferred to and applied in human models to find stabilizers or inhibitors of 14-3-3 interaction in human cellular pathways.
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138
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Ascher DB, Jubb HC, Pires DEV, Ochi T, Higueruelo A, Blundell TL. Protein-Protein Interactions: Structures and Druggability. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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139
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Lin RW, Yang CN, Ku S, Ho CJ, Huang SB, Yang MC, Chang HW, Lin CM, Hwang J, Chen YL, Tzeng CC, Wang C. CFS-1686 causes cell cycle arrest at intra-S phase by interference of interaction of topoisomerase 1 with DNA. PLoS One 2014; 9:e113832. [PMID: 25460368 PMCID: PMC4252032 DOI: 10.1371/journal.pone.0113832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/30/2014] [Indexed: 01/07/2023] Open
Abstract
CFS-1686 (chemical name (E)-N-(2-(diethylamino)ethyl)-4-(2-(2-(5-nitrofuran-2-yl)vinyl)quinolin-4-ylamino)benzamide) inhibits cell proliferation and triggers late apoptosis in prostate cancer cell lines. Comparing the effect of CFS-1686 on cell cycle progression with the topoisomerase 1 inhibitor camptothecin revealed that CFS-1686 and camptothecin reduced DNA synthesis in S-phase, resulting in cell cycle arrest at the intra-S phase and G1-S boundary, respectively. The DNA damage in CFS-1686 and camptothecin treated cells was evaluated by the level of ATM phosphorylation, γH2AX, and γH2AX foci, showing that camptothecin was more effective than CFS-1686. However, despite its lower DNA damage capacity, CFS-1686 demonstrated 4-fold higher inhibition of topoisomerase 1 than camptothecin in a DNA relaxation assay. Unlike camptothecin, CFS-1686 demonstrated no activity on topoisomerase 1 in a DNA cleavage assay, but nevertheless it reduced the camptothecin-induced DNA cleavage of topoisomerase 1 in a dose-dependent manner. Our results indicate that CFS-1686 might bind to topoisomerase 1 to inhibit this enzyme from interacting with DNA relaxation activity, unlike campothecin's induction of a topoisomerase 1-DNA cleavage complex. Finally, we used a computer docking strategy to localize the potential binding site of CFS-1686 to topoisomerase 1, further indicating that CFS-1686 might inhibit the binding of Top1 to DNA.
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Affiliation(s)
- Ru-Wei Lin
- Bone and Joint Research Center, National Cheng Kung University, Tainan, Taiwan
- Medical Device R & D Core Laboratory, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Chia-Ning Yang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - ShengYu Ku
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Jung Ho
- Department of Orthopedics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shih-Bo Huang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Min-Chi Yang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Wen Chang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Chun-Mao Lin
- Department of Biochemistry, School of Medical, Taipei Medical University, Taipei, Taiwan
| | - Jaulang Hwang
- Department of Biochemistry, School of Medical, Taipei Medical University, Taipei, Taiwan
| | - Yeh-Long Chen
- Department of Medical and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cherg-Chyi Tzeng
- Department of Medical and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chihuei Wang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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140
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Lindsey RH, Pendleton M, Ashley RE, Mercer SL, Deweese JE, Osheroff N. Catalytic core of human topoisomerase IIα: insights into enzyme-DNA interactions and drug mechanism. Biochemistry 2014; 53:6595-602. [PMID: 25280269 PMCID: PMC4204876 DOI: 10.1021/bi5010816] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Coordination between the N-terminal gate and the catalytic core of topoisomerase II allows the proper capture, cleavage, and transport of DNA during the catalytic cycle. Because the activities of these domains are tightly linked, it has been difficult to discern their individual contributions to enzyme-DNA interactions and drug mechanism. To further address the roles of these domains, we analyzed the activity of the catalytic core of human topoisomerase IIα. The catalytic core and the wild-type enzyme both maintained higher levels of cleavage with negatively (as compared to positively) supercoiled plasmid, indicating that the ability to distinguish supercoil handedness is embedded within the catalytic core. However, the catalytic core alone displayed little ability to cleave DNA substrates that did not intrinsically provide the enzyme with a transport segment (i.e., substrates that did not contain crossovers). Finally, in contrast to interfacial topoisomerase II poisons, covalent poisons did not enhance DNA cleavage mediated by the catalytic core. This distinction allowed us to further characterize the mechanism of etoposide quinone, a drug metabolite that functions primarily as a covalent poison. Etoposide quinone retained some ability to enhance DNA cleavage mediated by the catalytic core, indicating that it still can function as an interfacial poison. These results further define the distinct contributions of the N-terminal gate and the catalytic core to topoisomerase II function. The catalytic core senses the handedness of DNA supercoils during cleavage, while the N-terminal gate is critical for capturing the transport segment and for the activity of covalent poisons.
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Affiliation(s)
- R Hunter Lindsey
- Department of Biochemistry, ‡Department of Pharmacology, and §Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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141
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Structure-based design, synthesis and biological testing of etoposide analog epipodophyllotoxin-N-mustard hybrid compounds designed to covalently bind to topoisomerase II and DNA. Bioorg Med Chem 2014; 22:5935-49. [PMID: 25282653 DOI: 10.1016/j.bmc.2014.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/27/2014] [Accepted: 09/08/2014] [Indexed: 01/08/2023]
Abstract
Drugs that target DNA topoisomerase II isoforms and alkylate DNA represent two mechanistically distinct and clinically important classes of anticancer drugs. Guided by molecular modeling and docking a series of etoposide analog epipodophyllotoxin-N-mustard hybrid compounds were designed, synthesized and biologically characterized. These hybrids were designed to alkylate nucleophilic protein residues on topoisomerase II and thus produce inactive covalent adducts and to also alkylate DNA. The most potent hybrid had a mean GI(50) in the NCI-60 cell screen 17-fold lower than etoposide. Using a variety of in vitro and cell-based assays all of the hybrids tested were shown to target topoisomerase II. A COMPARE analysis indicated that the hybrids had NCI 60-cell growth inhibition profiles matching both etoposide and the N-mustard compounds from which they were derived. These results supported the conclusion that the hybrids displayed characteristics that were consistent with having targeted both topoisomerase II and DNA.
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142
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Pedley AM, Lill MA, Davisson VJ. Flexibility of PCNA-protein interface accommodates differential binding partners. PLoS One 2014; 9:e102481. [PMID: 25036435 PMCID: PMC4103810 DOI: 10.1371/journal.pone.0102481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022] Open
Abstract
The expanding roles of PCNA in functional assembly of DNA replication and repair complexes motivated investigation of the structural and dynamic properties guiding specificity of PCNA-protein interactions. A series of biochemical and computational analyses were combined to evaluate the PIP Box recognition features impacting complex formation. The results indicate subtle differences in topological and molecular descriptors distinguishing both affinity and stoichiometry of binding among PCNA-peptide complexes through cooperative effects. These features were validated using peptide mimics of p85α and Akt, two previously unreported PCNA binding partners. This study characterizes for the first time a reverse PIP Box interaction with PCNA. Small molecule ligand binding at the PIP Box interaction site confirmed the adaptive nature of the protein in dictating overall shape and implicates allosterism in transmitting biological effects.
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Affiliation(s)
- Anthony M. Pedley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - V. Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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143
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Abstract
TDP1 and TDP2 were discovered and named based on the fact they process 3'- and 5'-DNA ends by excising irreversible protein tyrosyl-DNA complexes involving topoisomerases I and II, respectively. Yet, both enzymes have an extended spectrum of activities. TDP1 not only excises trapped topoisomerases I (Top1 in the nucleus and Top1mt in mitochondria), but also repairs oxidative damage-induced 3'-phosphoglycolates and alkylation damage-induced DNA breaks, and excises chain terminating anticancer and antiviral nucleosides in the nucleus and mitochondria. The repair function of TDP2 is devoted to the excision of topoisomerase II- and potentially topoisomerases III-DNA adducts. TDP2 is also essential for the life cycle of picornaviruses (important human and bovine pathogens) as it unlinks VPg proteins from the 5'-end of the viral RNA genome. Moreover, TDP2 has been involved in signal transduction (under the former names of TTRAP or EAPII). The DNA repair partners of TDP1 include PARP1, XRCC1, ligase III and PNKP from the base excision repair (BER) pathway. By contrast, TDP2 repair functions are coordinated with Ku and ligase IV in the non-homologous end joining pathway (NHEJ). This article summarizes and compares the biochemistry, functions, and post-translational regulation of TDP1 and TDP2, as well as the relevance of TDP1 and TDP2 as determinants of response to anticancer agents. We discuss the rationale for developing TDP inhibitors for combinations with topoisomerase inhibitors (topotecan, irinotecan, doxorubicin, etoposide, mitoxantrone) and DNA damaging agents (temozolomide, bleomycin, cytarabine, and ionizing radiation), and as novel antiviral agents.
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Affiliation(s)
- Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA.
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Rui Gao
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku 606-8501, Japan
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
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Khiati S, Seol Y, Agama K, Dalla Rosa I, Agrawal S, Fesen K, Zhang H, Neuman KC, Pommier Y. Poisoning of mitochondrial topoisomerase I by lamellarin D. Mol Pharmacol 2014; 86:193-9. [PMID: 24890608 DOI: 10.1124/mol.114.092833] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Lamellarin D (Lam-D) is a hexacyclic pyrole alkaloid isolated from marine invertebrates, whose biologic properties have been attributed to mitochondrial targeting. Mitochondria contain their own DNA (mtDNA), and the only specific mitochondrial topoisomerase in vertebrates is mitochondrial topoisomerase I (Top1mt). Here, we show that Top1mt is a direct mitochondrial target of Lam-D. In vitro Lam-D traps Top1mt and induces Top1mt cleavage complexes (Top1mtcc). Using single-molecule analyses, we also show that Lam-D slows down supercoil relaxation of Top1mt and strongly inhibits Top1mt religation in contrast to the inefficacy of camptothecin on Top1mt. In living cells, we show that Lam-D accumulates rapidly inside mitochondria, induces cellular Top1mtcc, and leads to mtDNA damage. This study provides evidence that Top1mt is a direct mitochondrial target of Lam-D and suggests that developing Top1mt inhibitors represents a novel strategy for targeting mitochondrial DNA.
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Affiliation(s)
- Salim Khiati
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Yeonee Seol
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Ilaria Dalla Rosa
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Surbhi Agrawal
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Katherine Fesen
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Keir C Neuman
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (S.K., K.A., I.D.R., S.A., K.F., H.Z., Y.P.) and Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute (Y.S., K.C.N.), National Institutes of Health, Bethesda, Maryland
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145
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Pandey KK, Bera S, Korolev S, Campbell M, Yin Z, Aihara H, Grandgenett DP. Rous sarcoma virus synaptic complex capable of concerted integration is kinetically trapped by human immunodeficiency virus integrase strand transfer inhibitors. J Biol Chem 2014; 289:19648-58. [PMID: 24872410 DOI: 10.1074/jbc.m114.573311] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We determined conditions to produce milligram quantities of the soluble Rous sarcoma virus (RSV) synaptic complex that is kinetically trapped by HIV strand transfer inhibitors (STIs). Concerted integration catalyzed by RSV integrase (IN) is effectively inhibited by HIV STIs. Optimized assembly of the RSV synaptic complex required IN, a gain-of-function 3'-OH-recessed U3 oligonucleotide, and an STI under specific conditions to maintain solubility of the trapped synaptic complex at 4 °C. A C-terminal truncated IN (1-269 residues) produced a homogeneous population of trapped synaptic complex that eluted at ∼ 151,000 Da upon Superdex 200 size-exclusion chromatography (SEC). Approximately 90% of input IN and DNA are incorporated into the trapped synaptic complex using either the C-terminally truncated IN or wild type IN (1-286 residues). No STI is present in the SEC running buffer suggesting the STI-trapped synaptic complex is kinetically stabilized. The yield of the trapped synaptic complex correlates with the dissociative half-life of the STI observed with HIV IN-DNA complexes. Dolutegravir, MK-2048, and MK-0536 are equally effective, whereas raltegravir is ∼ 70% as effective. Without an STI present in the assembly mixture, no trapped synaptic complex was observed. Fluorescence and mass spectroscopy analyses demonstrated that the STI remains associated with the trapped complex. SEC-multiangle light scattering analyses demonstrated that wild type IN and the C-terminal IN truncation are dimers that acted as precursors to the tetramer. The purified STI-trapped synaptic complex contained a tetramer as shown by cross-linking studies. Structural studies of this three-domain RSV IN in complex with viral DNA may be feasible.
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Affiliation(s)
| | - Sibes Bera
- From the Institute for Molecular Virology
| | | | - Mary Campbell
- Center for World Health and Medicine, Saint Louis University Health Sciences Center, Saint Louis, Missouri 63104 and
| | - Zhiqi Yin
- the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Hideki Aihara
- the Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
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146
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Liu N, He QM, Chen JW, Li YQ, Xu YF, Ren XY, Sun Y, Mai HQ, Shao JY, Jia WH, Kang TB, Zeng MS, Ma J. Overexpression of CIP2A is an independent prognostic indicator in nasopharyngeal carcinoma and its depletion suppresses cell proliferation and tumor growth. Mol Cancer 2014; 13:111. [PMID: 24884612 PMCID: PMC4046003 DOI: 10.1186/1476-4598-13-111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancerous inhibitor of protein phosphatase 2A (CIP2A) is an oncoprotein that acts as a prognostic marker for several human malignancies. In this study, we investigated the clinical significance of CIP2A and its function in nasopharyngeal carcinoma (NPC). METHODS Quantitative RT-PCR, western blot, and immunohistochemistry analyses were used to quantify CIP2A expression in NPC cell lines and clinical samples. Kaplan-Meier curves were used to estimate the association between CIP2A expression and patient survival. The functional role of CIP2A in NPC cell lines was evaluated by small interfering RNA-mediated depletion of the protein followed by analyses of cell proliferation and xenograft growth. RESULTS CIP2A levels were upregulated in NPC cell lines and clinical samples at both the mRNA and protein levels (P < 0.01). Patients with high CIP2A expression had poorer overall survival (HR, 1.98; 95% CI, 1.16-3.34; P = 0.01) and poorer disease-free survival (HR, 1.68; 95% CI, 1.07-2.62; P = 0.02) rates than patients with low CIP2A expression. In addition, CIP2A expression status was an independent prognostic indicator for NPC patients. The depletion of CIP2A expression inhibited c-Myc protein expression in NPC cell lines, suppressed cell viability, colony formation, and anchorage-independent growth in vitro, and inhibited xenograft tumor growth in vivo. CONCLUSIONS Our data demonstrate that high CIP2A expression in patients was associated with poor survival in NPC, and depletion of CIP2A expression inhibited NPC cell proliferation and tumor growth. Thus, these results warrant further investigation of CIP2A as a novel therapeutic target for the treatment of NPC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jun Ma
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center of Cancer Medicine, 651 Dongfeng Road East, Guangzhou, People's Republic of China.
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147
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Gao R, Schellenberg MJ, Huang SYN, Abdelmalak M, Marchand C, Nitiss KC, Nitiss JL, Williams RS, Pommier Y. Proteolytic degradation of topoisomerase II (Top2) enables the processing of Top2·DNA and Top2·RNA covalent complexes by tyrosyl-DNA-phosphodiesterase 2 (TDP2). J Biol Chem 2014; 289:17960-9. [PMID: 24808172 DOI: 10.1074/jbc.m114.565374] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic type II topoisomerases (Top2α and Top2β) are homodimeric enzymes; they are essential for altering DNA topology by the formation of normally transient double strand DNA cleavage. Anticancer drugs (etoposide, doxorubicin, and mitoxantrone) and also Top2 oxidation and DNA helical alterations cause potentially irreversible Top2·DNA cleavage complexes (Top2cc), leading to Top2-linked DNA breaks. Top2cc are the therapeutic mechanism for killing cancer cells. Yet Top2cc can also generate recombination, translocations, and apoptosis in normal cells. The Top2 protein-DNA covalent complexes are excised (in part) by tyrosyl-DNA-phosphodiesterase 2 (TDP2/TTRAP/EAP2/VPg unlinkase). In this study, we show that irreversible Top2cc induced in suicidal substrates are not processed by TDP2 unless they first undergo proteolytic processing or denaturation. We also demonstrate that TDP2 is most efficient when the DNA attached to the tyrosyl is in a single-stranded configuration and that TDP2 can efficiently remove a tyrosine linked to a single misincorporated ribonucleotide or to polyribonucleotides, which expands the TDP2 catalytic profile with RNA substrates. The 1.6-Å resolution crystal structure of TDP2 bound to a substrate bearing a 5'-ribonucleotide defines a mechanism through which RNA can be accommodated in the TDP2 active site, albeit in a strained conformation.
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Affiliation(s)
- Rui Gao
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew J Schellenberg
- the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Shar-Yin N Huang
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Monica Abdelmalak
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Christophe Marchand
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Karin C Nitiss
- the Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, Illinois 61107
| | - John L Nitiss
- the Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, Illinois 61107
| | - R Scott Williams
- the Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, and
| | - Yves Pommier
- From the Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892,
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148
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Lv PC, Agama K, Marchand C, Pommier Y, Cushman M. Design, synthesis, and biological evaluation of O-2-modified indenoisoquinolines as dual topoisomerase I-tyrosyl-DNA phosphodiesterase I inhibitors. J Med Chem 2014; 57:4324-36. [PMID: 24800942 PMCID: PMC4033654 DOI: 10.1021/jm500294a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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Tyrosyl-DNA
phosphodiesterase I (TDP1) repairs stalled topoisomerase
I (Top1)–DNA covalent complexes and has been proposed to be
a promising and attractive target for cancer treatment. Inhibitors
of TDP1 could conceivably act synergistically with Top1 inhibitors
and thereby potentiate the effects of Top1 poisons. This study describes
the successful design and synthesis of 2-position-modified indenoisoquinolines
as dual Top1–TDP1 inhibitors using a structure-based drug design
approach. Enzyme inhibition studies indicate that indenoisoquinolines
modified at the 2-position with three-carbon side chains ending with
amino substituents show both promising Top1 and TDP1 inhibitory activity.
Molecular modeling of selected target compounds bound to Top1 and
TDP1 was used to rationalize the enzyme inhibition results and structure–activity
relationship analysis.
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Affiliation(s)
- Peng-Cheng Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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149
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Dalla Rosa I, Huang SYN, Agama K, Khiati S, Zhang H, Pommier Y. Mapping topoisomerase sites in mitochondrial DNA with a poisonous mitochondrial topoisomerase I (Top1mt). J Biol Chem 2014; 289:18595-602. [PMID: 24798329 DOI: 10.1074/jbc.m114.555367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial topoisomerase I (Top1mt) is a type IB topoisomerase present in vertebrates and exclusively targeted to mitochondria. Top1mt relaxes mitochondrial DNA (mtDNA) supercoiling by introducing transient cleavage complexes wherein the broken DNA strand swivels around the intact strand. Top1mt cleavage complexes (Top1mtcc) can be stabilized in vitro by camptothecin (CPT). However, CPT does not trap Top1mtcc efficiently in cells and is highly cytotoxic due to nuclear Top1 targeting. To map Top1mtcc on mtDNA in vivo and to overcome the limitations of CPT, we designed two substitutions (T546A and N550H) in Top1mt to stabilize Top1mtcc. We refer to the double-mutant enzyme as Top1mt*. Using retroviral transduction and ChIP-on-chip assays with Top1mt* in Top1mt knock-out murine embryonic fibroblasts, we demonstrate that Top1mt* forms high levels of cleavage complexes preferentially in the noncoding regulatory region of mtDNA, accumulating especially at the heavy strand replication origin OH, in the ribosomal genes (12S and 16S) and at the light strand replication origin OL. Expression of Top1mt* also caused rapid mtDNA depletion without affecting mitochondria mass, suggesting the existence of specific mitochondrial pathways for the removal of damaged mtDNA.
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Affiliation(s)
- Ilaria Dalla Rosa
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Shar-Yin N Huang
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Keli Agama
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Salim Khiati
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Hongliang Zhang
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yves Pommier
- From the Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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150
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Smith NA, Byl JAW, Mercer SL, Deweese JE, Osheroff N. Etoposide quinone is a covalent poison of human topoisomerase IIβ. Biochemistry 2014; 53:3229-36. [PMID: 24766193 PMCID: PMC4033626 DOI: 10.1021/bi500421q] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Etoposide is a topoisomerase II poison
that is utilized to treat
a broad spectrum of human cancers. Despite its wide clinical use,
2–3% of patients treated with etoposide eventually develop
treatment-related acute myeloid leukemias (t-AMLs) characterized by
rearrangements of the MLL gene. The molecular basis
underlying the development of these t-AMLs is not well understood;
however, previous studies have implicated etoposide metabolites (i.e.,
etoposide quinone) and topoisomerase IIβ in the leukemogenic
process. Although interactions between etoposide quinone and topoisomerase
IIα have been characterized, the effects of the drug metabolite
on the activity of human topoisomerase IIβ have not been reported.
Thus, we examined the ability of etoposide quinone to poison human
topoisomerase IIβ. The quinone induced ∼4 times more
enzyme-mediated DNA cleavage than did the parent drug. Furthermore,
the potency of etoposide quinone was ∼2 times greater against
topoisomerase IIβ than it was against topoisomerase IIα,
and the drug reacted ∼2–4 times faster with the β
isoform. Etoposide quinone induced a higher ratio of double- to single-stranded
breaks than etoposide, and its activity was less dependent on ATP.
Whereas etoposide acts as an interfacial topoisomerase II poison,
etoposide quinone displayed all of the hallmarks of a covalent poison:
the activity of the metabolite was abolished by reducing agents, and
the compound inactivated topoisomerase IIβ when it was incubated
with the enzyme prior to the addition of DNA. These results are consistent
with the hypothesis that etoposide quinone contributes to etoposide-related
leukemogenesis through an interaction with topoisomerase IIβ.
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Affiliation(s)
- Nicholas A Smith
- Departments of †Biochemistry, ‡Medicine (Hematology/Oncology), and §Pharmacology, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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