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Zhao Y, Hisayoshi T, Zhang D, Suzuki S, Watanabe T, Kobayashi A, Guo Q, Momozawa Y, Shimokawa T, Kato S, Miki Y, Sunada S. Steroid-Modulated Transcription Synergistically Forms DNA Double-Strand Breaks With Topoisomerase II Inhibitor. Cancer Sci 2025. [PMID: 40231641 DOI: 10.1111/cas.70081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 03/20/2025] [Accepted: 04/05/2025] [Indexed: 04/16/2025] Open
Abstract
The synergistic effects of drug combinations have emerged as a promising approach for achieving efficient cancer treatment. Through our exploration of drug combinations, we found that medroxyprogesterone acetate (MPA), a steroid, induced a synergistic antitumor effect in combination with the topoisomerase II inhibitor etoposide (ETP). In this study, we investigated the mechanisms underlying this synergistic effect for potential clinical applications. To elucidate the relevant mechanisms, we performed a cell viability assay, cell cycle analysis, DNA repair assays, detection of DNA double-strand breaks (DSBs) and the nuclear localization of topoisomerase II (Top2), and genome-wide detection of DSBs. MPA synergistically increased ETP-induced DSBs, resulting in cell cycle arrest in the G2/M phase. Interestingly, this effect was not due to the inhibition of DSB repair but to a specific increase in the Top2-DNA covalent complex formed by ETP. A genome-wide search for DSB locations revealed that DSB formation was promoted near promoter regions, suggesting the involvement of MPA transcriptional modulation in this mechanism. We also found that various steroids promoted DSB formation when combined with ETP, strongly supporting our synergistic model. Therefore, this synergistic effect is based on an innovative mechanism that differs from conventional strategies targeting the DNA damage response and is expected to contribute toward novel therapeutic options.
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Affiliation(s)
- Ying Zhao
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tetsuro Hisayoshi
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Doudou Zhang
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Saaya Suzuki
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takashi Watanabe
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Qianqian Guo
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Takashi Shimokawa
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Shunsuke Kato
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshio Miki
- Research and Development Center for Precision Medicine, University of Tsukuba, Ibaraki, Japan
| | - Shigeaki Sunada
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Clinical Oncology, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Juntendo Advanced Research Institute for Health Science, Juntendo University, Tokyo, Japan
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2
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Chang JW, O’Brian AK, Thomas AJ, Hardin MR, Latham BD, Ngabonziza D, Simpson LG, Wade BD, Kühnhenrich L, Thompson NM, Endsley CE, Deweese JE. Mutagenesis of Intrinsically Disordered Domain Impacts Topoisomerase IIα Catalytic Activity. Int J Mol Sci 2025; 26:3604. [PMID: 40332112 PMCID: PMC12026768 DOI: 10.3390/ijms26083604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/08/2025] [Accepted: 04/08/2025] [Indexed: 05/08/2025] Open
Abstract
Human topoisomerase IIα and IIβ regulate DNA topology and knots in chromosomes during crucial cellular processes, making these enzymes common targets for anticancer drugs. However, selective inhibition of topoisomerase IIα (TOP2A) is desired to decrease adverse effects, which may be mediated by topoisomerase IIβ (TOP2B). The main region of difference between the two isoforms is the intrinsically disordered C-terminal domain (CTD), which is being studied as a target for selective inhibition. Our previous work examined several regions within the CTD to determine whether those regions impact biochemical function. In this current study, we designed and constructed four TOP2A mutants with amino acid substitutions in the CTD, which were then assessed for impact on biochemical activity. V1482D exhibited increased levels of relaxation, while both V1482D and K1520I exhibited increased levels of decatenation. No major impact on DNA cleavage or binding were observed with any of the mutants. The isolated impact of the changes on relaxation and decatenation supports the concept that the CTD can affect one aspect of the enzyme's function in an isolated manner, which was seen in our previous study. Taken together, these results suggest that modification of specific positions within the CTD affects substrate selection. These results are mapped onto the CTD for consideration of potential regions to target for inhibition of TOP2A.
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Affiliation(s)
- Jeong Won Chang
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Addison K. O’Brian
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Allison J. Thomas
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Mattalyn R. Hardin
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Brooke D. Latham
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Daniel Ngabonziza
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Lily G. Simpson
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Benjamin D. Wade
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Laura Kühnhenrich
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Nina M. Thompson
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Clark E. Endsley
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Joseph E. Deweese
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
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3
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Gupta A, Parveen D, Azam F, Shaquiquzzaman M, Akhter M, Jaremko M, Emwas AH, Khan MA, Parvez S, Khanna S, Palit R, Jahangir U, Alam MM. Mechanistic insights into novel cyano-pyrimidine pendant chalcone derivatives as LSD1 inhibitors by docking, ADMET, MM/GBSA, and molecular dynamics simulation. Biochem Biophys Rep 2025; 41:101937. [PMID: 40028038 PMCID: PMC11871483 DOI: 10.1016/j.bbrep.2025.101937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Revised: 01/15/2025] [Accepted: 01/26/2025] [Indexed: 03/05/2025] Open
Abstract
Cancer presents a formidable and complex foe, standing as one of the foremost contributors to disease-related fatalities across the globe. According to data from the Global Cancer Observatory (GLOBOCAN), projections indicate a staggering 28.4 million cases of cancer, encompassing both new diagnoses and deaths, by 2040. Therefore, developing effective and comprehensive treatment approaches for cancer patients is essential and the conventional approved treatments for cancers are associated with various harmful side effects. Our study aims to address the critical and widespread need for alternative therapies that can effectively combat cancer with minimal side effects. The present contribution outlines a targeted approach using Lysine Specific Demethylase 1 (LSD1) to evaluate novel cyano-pyrimidine pendant chalcone derivatives as potential antiproliferative agents. Two sets of novel cyano-pyrimidine pendant chalcone derivatives were produced, and molecular docking was performed on the LSD1 protein. The ligands A1 and B1 belonging to series A and B, respectively, were found to have the highest docking scores of -11.095 and -10.773 kcal/mol, in that order. The ADME and toxicity studies of the ligands showed promising responses with respect to various pharmacokinetic and physicochemical parameters. The Molecular dynamics (MD) simulation results indicated effective diffusion of both complexes inside the protein cavity, facilitated by prominent interactions with various amino acids. Additionally, the complexes displayed high relative binding free energy. The computational screening of ligands indicates that ligands A1 and B1 exhibit potential for further exploration using various in vitro and in vivo techniques. These ligands may then serve as promising leads in the discovery of cancer drugs. The in-silico screening of the novel library of cyano-pyrimidine pendant chalcone derivatives was performed with a combination of molecular docking, MM-GBSA, ADME, toxicity and MD simulation. Molecular docking and MM-GBSA were conducted using the Glide and Prime tools, respectively, of the Schrödinger suite 12.8. The ligands were analysed for ADME using the Swiss ADME, while toxicity risks were evaluated using Osiris Property Explorer. Additionally, a 400ns MD simulation of LIGA1 and LIGB1 against the protein LSD1 was performed using the Desmond tool of Schrödinger suite 12.8 to validate the docking results and analyse the behaviour and stability of the complexes.
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Affiliation(s)
- Amisha Gupta
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Darakhshan Parveen
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Faizul Azam
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah, 51452, Saudi Arabia
| | - M. Shaquiquzzaman
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mymoona Akhter
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Mohammad Ahmed Khan
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 62, India
| | - Suruchi Khanna
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
| | - Rituparna Palit
- Department of Pharmaceutical Chemistry, RKGIT, AKTU, Uttar Pradesh, India
| | - Umar Jahangir
- Department of Amraz-e-Jild, School of Unani Medical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - M. Mumtaz Alam
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, 110062, India
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4
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Gedeon A, Yab E, Dinut A, Sadowski E, Capton E, Dreneau A, Petit J, Gioia B, Piveteau C, Djaout K, Lecat E, Wehenkel AM, Gubellini F, Mechaly A, Alzari PM, Deprez B, Baulard A, Aubry A, Willand N, Petrella S. Molecular mechanism of a triazole-containing inhibitor of Mycobacterium tuberculosis DNA gyrase. iScience 2024; 27:110967. [PMID: 39429773 PMCID: PMC11489056 DOI: 10.1016/j.isci.2024.110967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/02/2024] [Accepted: 09/12/2024] [Indexed: 10/22/2024] Open
Abstract
Antimicrobial resistance remains a persistent and pressing public health concern. Here, we describe the synthesis of original triazole-containing inhibitors targeting the DNA gyrase, a well-validated drug target for developing new antibiotics. Our compounds demonstrate potent antibacterial activity against various pathogenic bacteria, with notable potency against Mycobacterium tuberculosis (Mtb). Moreover, one hit, compound 10a, named BDM71403, was shown to be more potent in Mtb than the NBTI of reference, gepotidacin. Mechanistic enzymology assays reveal a competitive interaction of BDM71403 with fluoroquinolones within the Mtb gyrase cleavage core. High-resolution cryo-electron microscopy structural analysis provides detailed insights into the ternary complex formed by the Mtb gyrase, double-stranded DNA, and either BDM71403 or gepotidacin, providing a rational framework to understand the superior in vitro efficacy on Mtb. This study highlights the potential of triazole-based scaffolds as promising gyrase inhibitors, offering new avenues for drug development in the fight against antimicrobial resistance.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Emilie Yab
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Aurelia Dinut
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Elodie Sadowski
- Cimi-Paris, INSERM U1135, Sorbonne Université, AP-HP. Sorbonne Université, Laboratoire de Bactériologie-Hygiène, CNR des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 75005 Paris, France
| | - Estelle Capton
- Cimi-Paris, INSERM U1135, Sorbonne Université, AP-HP. Sorbonne Université, Laboratoire de Bactériologie-Hygiène, CNR des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 75005 Paris, France
| | - Aurore Dreneau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Julienne Petit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Bruna Gioia
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Estelle Lecat
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Anne Marie Wehenkel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Cell Cycle Mechanisms Unit, 75015 Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Plate-Forme de Cristallographie, CNRS UMR 3528, 75015 Paris, France
| | - Pedro M. Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
| | - Benoît Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Alain Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Alexandra Aubry
- Cimi-Paris, INSERM U1135, Sorbonne Université, AP-HP. Sorbonne Université, Laboratoire de Bactériologie-Hygiène, CNR des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 75005 Paris, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Stéphanie Petrella
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Cell Cycle Mechanisms Unit, 75015 Paris, France
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5
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Nitiss KC, Bandak A, Berger JM, Nitiss JL. Genome Instability Induced by Topoisomerase Misfunction. Int J Mol Sci 2024; 25:10247. [PMID: 39408578 PMCID: PMC11477040 DOI: 10.3390/ijms251910247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/19/2024] [Accepted: 09/20/2024] [Indexed: 10/20/2024] Open
Abstract
Topoisomerases alter DNA topology by making transient DNA strand breaks (DSBs) in DNA. The DNA cleavage reaction mechanism includes the formation of a reversible protein/DNA complex that allows rapid resealing of the transient break. This mechanism allows changes in DNA topology with minimal risks of persistent DNA damage. Nonetheless, small molecules, alternate DNA structures, or mutations in topoisomerase proteins can impede the resealing of the transient breaks, leading to genome instability and potentially cell death. The consequences of high levels of enzyme/DNA adducts differ for type I and type II topoisomerases. Top1 action on DNA containing ribonucleotides leads to 2-5 nucleotide deletions in repeated sequences, while mutant Top1 enzymes can generate large deletions. By contrast, small molecules that target Top2, or mutant Top2 enzymes with elevated levels of cleavage lead to small de novo duplications. Both Top1 and Top2 have the potential to generate large rearrangements and translocations. Thus, genome instability due to topoisomerase mis-function is a potential pathogenic mechanism especially leading to oncogenic progression. Recent studies support the potential roles of topoisomerases in genetic changes in cancer cells, highlighting the need to understand how cells limit genome instability induced by topoisomerases. This review highlights recent studies that bear on these questions.
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Affiliation(s)
- Karin C. Nitiss
- Pharmaceutical Sciences Department, University of Illinois Chicago, Rockford, IL 61107, USA;
| | - Afif Bandak
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 20215, USA; (A.B.); (J.M.B.)
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 20215, USA; (A.B.); (J.M.B.)
| | - John L. Nitiss
- Pharmaceutical Sciences Department, University of Illinois Chicago, Rockford, IL 61107, USA;
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6
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Adly ME, Gedawy EM, El-Malah AA, Khalil OM. Design, synthesis and in vitro anticancer activity of some new lomefloxacin derivatives. Sci Rep 2024; 14:6175. [PMID: 38485748 PMCID: PMC10940605 DOI: 10.1038/s41598-024-56313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Our main goal was to design and synthesize novel lomefloxacin derivatives that inhibit the topoisomerase II enzyme, leading to potent anticancer activity. Lomefloxacin derivatives substituted at position 3 and 7 were synthesized and screened for cytotoxic activity utilizing 60 different human cancer cell lines. Furthermore, compounds 3a,b,c,e that revealed potent broad-spectrum anticancer activity (with mean percent GI more than 47%) were further evaluated using five dose concentrations and calculating the GI50. Compound 3e was then evaluated for cell cycle analysis and demonstrated cell cycle arrest at the G2-M phase. Moreover, the mechanism of action was determined by determining the topoisomerase inhibitory activity and the molecular modeling study. Compounds 3a,b,c,e showed broad spectrum anticancer activity. Lomefloxacin derivative 5f showed selective cytotoxic activity against melanoma SK-MEL-5 cell line. Compound 3e demonstrated comparable topoisomerase II inhibition to doxorubicin with IC50 of 0.98 µM.
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Affiliation(s)
- Mina E Adly
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt.
| | - Ehab M Gedawy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University in Cairo, Cairo, 11829, Egypt
| | - Afaf A El-Malah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Omneya M Khalil
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
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7
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Sobh EA, Kassab AE, El-Khouly EA, S A Hassan M. New pyranopyrazole based derivatives: Design, synthesis, and biological evaluation as potential topoisomerase II inhibitors, apoptotic inducers, and antiproliferative agents. Bioorg Chem 2024; 144:107158. [PMID: 38301427 DOI: 10.1016/j.bioorg.2024.107158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/06/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
A new series of pyranopyrazole-based derivatives were designed and synthesized. The synthesized compounds were assessed for their cytotoxic efficacy against A549 human lung carcinoma and MCF-7 human breast carcinoma cell lines. Three compounds (1b, 4b, and 7b) exhibited 1.3- to 2.3-fold more antiproliferative activity than that of doxorubicin against the A549 cell line. In comparison to doxorubicin, compounds 1d and 3b were 4.1- and 1.04-fold, respectively more powerful against MCF-7 cancer cells. All the synthesized compounds were found to be more selective toward A549 cancer cells than the normal human fibroblast BJ cells. Of interest, compounds 1b and 7b exhibited promising cytotoxicity and SIs of 27.72 and 25.30, respectively, towards A549 cancer cells, higher than that of doxorubicin (SI 4.81). The most potent compounds 1b, 1d, 3b, 4b, and 7b were then subjected to in vitro Topo II inhibition assay. They showed IC50 values in the range of 2.07 to 8.86 µM. Of particular interest, compound 7b (IC50 = 2.07 µM), exhibited higher Topo II inhibitory activity than that of doxorubicin (IC50 = 2.56 µM). The significant Topo II inhibition of compound 7b was explained by molecular docking simulations into the Topo II active site. Compound 7b halted the cell cycle in the S phase in A549 cancer cells. It induced total apoptosis and necrosis of 20.73- and 4-fold, respectively, greater than the control. This evidence was supported by a 3.59-fold increase in the level of apoptotic caspase-9 and a remarkable elevation of the Bax/BCL-2 ratio. The physiochemical parameters of compound 7b were aligned with Lipinski's rule of five.
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Affiliation(s)
- Eman A Sobh
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Menoufia University, Menoufia, Gamal Abd El-Nasir Street, Egypt
| | - Asmaa E Kassab
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Kasr El-Aini Street, 11562, Egypt.
| | - Eman A El-Khouly
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Kasr El-Aini Street, 11562, Egypt
| | - Marwa S A Hassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Kasr El-Aini Street, 11562, Egypt
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8
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Chatzinikolaou G, Stratigi K, Siametis A, Goulielmaki E, Akalestou-Clocher A, Tsamardinos I, Topalis P, Austin C, Bouwman BA, Crosetto N, Altmüller J, Garinis GA. XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes. SCIENCE ADVANCES 2023; 9:eadi2095. [PMID: 37939182 PMCID: PMC10631727 DOI: 10.1126/sciadv.adi2095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop-dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair-deficient syndromes associated with transcription-associated DNA damage.
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Affiliation(s)
- Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Tsamardinos
- Computer Science Department of University of Crete, Heraklion, Crete, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
| | - Caroline Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Britta A. M. Bouwman
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
| | - Nicola Crosetto
- Division of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Science for Life Laboratory, Stockholm 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157 Milan, Italy
| | - Janine Altmüller
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Facility Genomics, Charitéplatz 1, 10117 Berlin, Germany
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas, GR70013, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
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9
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Dauda SE, Collins JA, Byl JAW, Lu Y, Yalowich JC, Mitton-Fry MJ, Osheroff N. Actions of a Novel Bacterial Topoisomerase Inhibitor against Neisseria gonorrhoeae Gyrase and Topoisomerase IV: Enhancement of Double-Stranded DNA Breaks. Int J Mol Sci 2023; 24:12107. [PMID: 37569485 PMCID: PMC10419083 DOI: 10.3390/ijms241512107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are an emerging class of antibacterials that target gyrase and topoisomerase IV. A hallmark of NBTIs is their ability to induce gyrase/topoisomerase IV-mediated single-stranded DNA breaks and suppress the generation of double-stranded breaks. However, a previous study reported that some dioxane-linked amide NBTIs induced double-stranded DNA breaks mediated by Staphylococcus aureus gyrase. To further explore the ability of this NBTI subclass to increase double-stranded DNA breaks, we examined the effects of OSUAB-185 on DNA cleavage mediated by Neisseria gonorrhoeae gyrase and topoisomerase IV. OSUAB-185 induced single-stranded and suppressed double-stranded DNA breaks mediated by N. gonorrhoeae gyrase. However, the compound stabilized both single- and double-stranded DNA breaks mediated by topoisomerase IV. The induction of double-stranded breaks does not appear to correlate with the binding of a second OSUAB-185 molecule and extends to fluoroquinolone-resistant N. gonorrhoeae topoisomerase IV, as well as type II enzymes from other bacteria and humans. The double-stranded DNA cleavage activity of OSUAB-185 and other dioxane-linked NBTIs represents a paradigm shift in a hallmark characteristic of NBTIs and suggests that some members of this subclass may have alternative binding motifs in the cleavage complex.
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Affiliation(s)
- Soziema E. Dauda
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jessica A. Collins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jo Ann W. Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Jack C. Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 42310, USA
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, 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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10
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Byl JAW, Mueller R, Bax B, Basarab GS, Chibale K, Osheroff N. A Series of Spiropyrimidinetriones that Enhances DNA Cleavage Mediated by Mycobacterium tuberculosis Gyrase. ACS Infect Dis 2023; 9:706-715. [PMID: 36802491 PMCID: PMC10006343 DOI: 10.1021/acsinfecdis.3c00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The rise in drug-resistant tuberculosis has necessitated the search for alternative antibacterial treatments. Spiropyrimidinetriones (SPTs) represent an important new class of compounds that work through gyrase, the cytotoxic target of fluoroquinolone antibacterials. The present study analyzed the effects of a novel series of SPTs on the DNA cleavage activity of Mycobacterium tuberculosis gyrase. H3D-005722 and related SPTs displayed high activity against gyrase and increased levels of enzyme-mediated double-stranded DNA breaks. The activities of these compounds were similar to those of the fluoroquinolones, moxifloxacin, and ciprofloxacin and greater than that of zoliflodacin, the most clinically advanced SPT. All the SPTs overcame the most common mutations in gyrase associated with fluoroquinolone resistance and, in most cases, were more active against the mutant enzymes than wild-type gyrase. Finally, the compounds displayed low activity against human topoisomerase IIα. These findings support the potential of novel SPT analogues as antitubercular drugs.
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Affiliation(s)
- Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Rudolf Mueller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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11
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Olatunde OZ, Yong J, Lu C, Ming Y. A Review on Shikonin and Its Derivatives as Potent Anticancer Agents Targeted against Topoisomerases. Curr Med Chem 2023; 31:CMC-EPUB-129356. [PMID: 36752292 DOI: 10.2174/0929867330666230208094828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 02/09/2023]
Abstract
The topoisomerases (TOPO) play indispensable roles in DNA metabolism, by regulating the topological state of DNA. Topoisomerase I and II are the well-established drug-targets for the development of anticancer agents and antibiotics. These drugs-targeting enzymes have been used to establish the relationship between drug-stimulated DNA cleavable complex formation and cytotoxicity. Some anticancer drugs (such as camptothecin, anthracyclines, mitoxantrone) are also widely used as Topo I and Topo II inhibitors, but the poor water solubility, myeloma suppression, dose-dependent cardiotoxicity, and multidrug resistance (MDR) limited their prolong use as therapeutics. Also, most of these agents displayed selective inhibition only against Topo I or II. In recent years, researchers focus on the design and synthesis of the dual Topo I and II inhibitors, or the discovery of the dual Topo I and II inhibitors from natural products. Shikonin (a natural compound with anthraquinone skeleton, isolated from the roots of Lithospermum erythrorhizon) has drawn much attention due to its wide spectrum of anticancer activities, especially due to its dual Topo inhibitive performance, and without the adverse side effects, and different kinds of shikonin derivatives have been synthesized as TOPO inhibitors for the development of anticancer agents. In this review, the progress of the shikonin and its derivatives together with their anticancer activities, anticancer mechanism, and their structure-activity relationship (SAR) was comprehensively summarized by searching the CNKI, PubMed, Web of Science, Scopus, and Google Scholar databases.
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Affiliation(s)
- Olagoke Zacchaeus Olatunde
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian,350002, China
| | - Jianping Yong
- Xiamen Institute of Rare-earth Materials, Chinese Academy of Sciences, Xiamen, Fujian, 361021, China
| | - Canzhong Lu
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian,350002, China
- Xiamen Institute of Rare-earth Materials, Chinese Academy of Sciences, Xiamen, Fujian, 361021, China
| | - Yanlin Ming
- Fujian Institute of Subtropical Botany, Xiamen, Fujian, 361006, China
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12
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Carter HE, Wildman B, Schwanz HA, Kerns RJ, Aldred KJ. Role of the Water-Metal Ion Bridge in Quinolone Interactions with Escherichia coli Gyrase. Int J Mol Sci 2023; 24:2879. [PMID: 36769202 PMCID: PMC9917921 DOI: 10.3390/ijms24032879] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fluoroquinolones are an important class of antibacterials, and rising levels of resistance threaten their clinical efficacy. Gaining a more full understanding of their mechanism of action against their target enzymes-the bacterial type II topoisomerases gyrase and topoisomerase IV-may allow us to rationally design quinolone-based drugs that overcome resistance. As a step toward this goal, we investigated whether the water-metal ion bridge that has been found to mediate the major point of interaction between Escherichia coli topoisomerase IV and Bacillus anthracis topoisomerase IV and gyrase, as well as Mycobacterium tuberculosis gyrase, exists in E. coli gyrase. This is the first investigation of the water-metal ion bridge and its function in a Gram-negative gyrase. Evidence suggests that the water-metal ion bridge does exist in quinolone interactions with this enzyme and, unlike the Gram-positive B. anthracis gyrase, does use both conserved residues (serine and acidic) as bridge anchors. Furthermore, this interaction appears to play a positioning role. These findings raise the possibility that the water-metal ion bridge is a universal point of interaction between quinolones and type II topoisomerases and that it functions primarily as a binding contact in Gram-positive species and primarily as a positioning interaction in Gram-negative species. Future studies will explore this possibility.
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Affiliation(s)
- Hannah E. Carter
- Biology Department, University of Evansville, Evansville, IN 47722, USA
| | - Baylee Wildman
- Biology Department, University of Evansville, Evansville, IN 47722, USA
| | - Heidi A. Schwanz
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 42232, USA
| | - Robert J. Kerns
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, Iowa City, IA 42232, USA
| | - Katie J. Aldred
- Biology Department, University of Evansville, Evansville, IN 47722, USA
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13
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Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. SCIENCE ADVANCES 2022; 8:eadd4920. [PMID: 36322662 PMCID: PMC9629710 DOI: 10.1126/sciadv.add4920] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 06/09/2023]
Abstract
Type II topoisomerases (TOP2) are conserved regulators of chromatin topology that catalyze reversible DNA double-strand breaks (DSBs) and are essential for maintaining genomic integrity in diverse dynamic processes such as transcription, replication, and cell division. While controlled TOP2-mediated DSBs are an elegant solution to topological constraints of DNA, DSBs also contribute to the emergence of chromosomal translocations and mutations that drive cancer. The central importance of TOP2 enzymes as frontline chemotherapeutic targets is well known; however, their precise biological functions and impact in cancer development are still poorly understood. In this review, we provide an updated overview of TOP2A and TOP2B in the regulation of chromatin topology and transcription, and discuss the recent discoveries linking TOP2 activities with cancer pathogenesis.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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14
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Cao H, Zhang Y, Cai Y, Tang L, Gao F, Xu D, Kapranov P. Hotspots of single-strand DNA “breakome” are enriched at transcriptional start sites of genes. Front Mol Biosci 2022; 9:895795. [PMID: 36046604 PMCID: PMC9420937 DOI: 10.3389/fmolb.2022.895795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Single-strand breaks (SSBs) represent one of the most common types of DNA damage, yet not much is known about the genome landscapes of this type of DNA lesions in mammalian cells. Here, we found that SSBs are more likely to occur in certain positions of the human genome—SSB hotspots—in different cells of the same cell type and in different cell types. We hypothesize that the hotspots are likely to represent biologically relevant breaks. Furthermore, we found that the hotspots had a prominent tendency to be enriched in the immediate vicinity of transcriptional start sites (TSSs). We show that these hotspots are not likely to represent technical artifacts or be caused by common mechanisms previously found to cause DNA cleavage at promoters, such as apoptotic DNA fragmentation or topoisomerase type II (TOP2) activity. Therefore, such TSS-associated hotspots could potentially be generated using a novel mechanism that could involve preferential cleavage at cytosines, and their existence is consistent with recent studies suggesting a complex relationship between DNA damage and regulation of gene expression.
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15
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Xu G, Li Z, Ding Y, Shen Y. Discovery of 1,2-diphenylethene derivatives as human DNA topoisomerase II catalytic inhibitors and antitumor agents. Eur J Med Chem 2022; 243:114706. [DOI: 10.1016/j.ejmech.2022.114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
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16
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Khazeem MM, Casement JW, Schlossmacher G, Kenneth NS, Sumbung NK, Chan JYT, McGow JF, Cowell IG, Austin CA. TOP2B Is Required to Maintain the Adrenergic Neural Phenotype and for ATRA-Induced Differentiation of SH-SY5Y Neuroblastoma Cells. Mol Neurobiol 2022; 59:5987-6008. [PMID: 35831557 PMCID: PMC9463316 DOI: 10.1007/s12035-022-02949-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/23/2022] [Indexed: 12/13/2022]
Abstract
The neuroblastoma cell line SH-SY5Y is widely used to study retinoic acid (RA)-induced gene expression and differentiation and as a tool to study neurodegenerative disorders. SH-SY5Y cells predominantly exhibit adrenergic neuronal properties, but they can also exist in an epigenetically interconvertible alternative state with more mesenchymal characteristics; as a result, these cells can be used to study gene regulation circuitry controlling neuroblastoma phenotype. Using a combination of pharmacological inhibition and targeted gene inactivation, we have probed the requirement for DNA topoisomerase IIB (TOP2B) in RA-induced gene expression and differentiation and in the balance between adrenergic neuronal versus mesenchymal transcription programmes. We found that expression of many, but not all genes that are rapidly induced by ATRA in SH-SY5Y cells was significantly reduced in the TOP2B null cells; these genes include BCL2, CYP26A1, CRABP2, and NTRK2. Comparing gene expression profiles in wild-type versus TOP2B null cells, we found that long genes and genes expressed at a high level in WT SH-SY5Y cells were disproportionately dependent on TOP2B. Notably, TOP2B null SH-SY5Y cells upregulated mesenchymal markers vimentin (VIM) and fibronectin (FN1) and components of the NOTCH signalling pathway. Enrichment analysis and comparison with the transcription profiles of other neuroblastoma-derived cell lines supported the conclusion that TOP2B is required to fully maintain the adrenergic neural-like transcriptional signature of SH-SY5Y cells and to suppress the alternative mesenchymal epithelial-like epigenetic state.
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Affiliation(s)
- Mushtaq M Khazeem
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,National Center of Hematology, Mustansiriyah University, Baghdad, Iraq
| | - John W Casement
- Bioinformatics Support Unit, The Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - George Schlossmacher
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Niall S Kenneth
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nielda K Sumbung
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Janice Yuen Tung Chan
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jade F McGow
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Ian G Cowell
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Caroline A Austin
- The Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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17
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Structural and Biochemical Basis of Etoposide-Resistant Mutations in Topoisomerase IIα. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Etoposide is a widely used anticancer drug that targets type II topoisomerases, including topoisomerase IIα (TOP2A). TOP2A is a nuclear enzyme involved in regulating DNA topology through a double-strand passage mechanism. TOP2A is a homodimeric enzyme with two symmetrical active sites formed by residues from either half of the dimer. Both active sites cleave DNA, forming an enzyme-bound, double-stranded DNA break. Etoposide acts by binding in the active site between the ends of cleaved DNA, preventing the enzyme from ligating the DNA. In the present study, biochemical and structural data are used to examine the mechanism of etoposide resistance found with specific point mutations in TOP2A. Mutations near the active site (D463A, G534R, R487K), along with some outside of the active site (ΔA429 and P716L), are examined. We hypothesize that changes in the coordination of DNA cleavage results from mutations that impact symmetrical relationships in the active site and surrounding regions. In some cases, we report the first data on purified versions of these enzymes. Based upon our results, both local and long-distance factors can impact etoposide action and may indicate interdependent relationships in structure and function.
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18
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Identification of a novel catalytic inhibitor of topoisomerase II alpha that engages distinct mechanisms in p53 wt or p53 -/- cells to trigger G2/M arrest and senescence. Cancer Lett 2022; 526:284-303. [PMID: 34843865 DOI: 10.1016/j.canlet.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/10/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022]
Abstract
We report a novel topoisomerase IIα inhibitor, mercaptopyridine oxide (MPO), which induces G2/M arrest and senescence with distinctly different cell cycle regulators (p21 or p14ARF) in HCT116p 53WT and HCT116 p53-/- cells, respectively. MPO treatment induced defective topoisomerase IIα-mediated decatenation process and inhibition of the enzyme's catalytic activity that stalled entry into mitosis. Topoisomerase IIα inhibition was associated with ROS-mediated activation of ATM-Chk2 kinase axis in HCT116 p53WT cells, but not in HCT116 p53-/- cells displaying early Chk1 activation. Results suggest that E2F1 stabilization might link MPO-induced p53 phospho-activation in HCT116 p53WT cells or p14ARF induction in HCT116 p53-/- cells. Also, interaction between topoisomerase IIα and Chk1 was induced in both cell lines, which could be important for decatenation checkpoint activation, even upon p53 ablation. Notably, TCGA dataset analyses revealed topoisomerase IIα upregulation across a wide array of cancers, which was associated with lower overall survival. Corroborating that increased topoisomerase IIα expression might offer susceptibility to the novel inhibitor, MPO (5 μM) induced strong inhibition in colony forming ability of pancreatic and hepatocellular cancer cell lines. These data highlight a novel topoisomerase IIα inhibitor and provide proof-of-concept for its therapeutic potential against cancers even with loss-of-function of p53.
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19
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Hwang SY, Shrestha A, Park S, Bist G, Kunwar S, Kadayat TM, Jang H, Seo M, Sheen N, Kim S, Jeon KH, Lee ES, Kwon Y. Identification of new halogen-containing 2,4-diphenyl indenopyridin-5-one derivative as a boosting agent for the anticancer responses of clinically available topoisomerase inhibitors. Eur J Med Chem 2022; 227:113916. [PMID: 34678573 DOI: 10.1016/j.ejmech.2021.113916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022]
Abstract
Based on previous reports on the significance of halogen moieties and the indenopyridin-5-one skeleton, we designed and synthesized a novel series of halogen (F-, Cl-, Br-, CF3- and OCF3-)-containing 2,4-diphenyl indenopyridin-5-ones and their corresponding -5-ols. Unlike indenopyridin-5-ols, most of the prepared indenopyridin-5-ones with Cl-, Br-, and CF3- groups at the 2-phenyl ring conferred a strong dual topoisomerase I/IIα inhibitory effect. Among the series, para-bromophenyl substituted compound 9 exhibited the most potent topoisomerase inhibition and antiproliferative effects, which showed dependency upon the topoisomerase gene expression level of diverse cancer cells. In particular, as a DNA minor groove-binding non-intercalative topoisomerase I/IIα catalytic inhibitor, compound 9 synergistically promoted the anticancer efficacy of clinically applied topoisomerase I/IIα poisons both in vitro and in vivo, having the great advantage of alleviating poison-related toxicities.
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Affiliation(s)
- Soo-Yeon Hwang
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Aarajana Shrestha
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Seojeong Park
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Ganesh Bist
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Surendra Kunwar
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Tara Man Kadayat
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Haejin Jang
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Minjung Seo
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Naeun Sheen
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Seojeong Kim
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kyung-Hwa Jeon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Eung-Seok Lee
- College of Pharmacy, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea.
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20
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Parra-Nunez P, Cooper C, Sanchez-Moran E. The Role of DNA Topoisomerase Binding Protein 1 (TopBP1) in Genome Stability in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122568. [PMID: 34961037 PMCID: PMC8706423 DOI: 10.3390/plants10122568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 05/17/2023]
Abstract
DNA topoisomerase II (TOPII) plays a very important role in DNA topology and in different biological processes such as DNA replication, transcription, repair, and chromosome condensation in higher eukaryotes. TOPII has been found to interact directly with a protein called topoisomerase II binding protein 1 (TopBP1) which also seems to have important roles in DNA replication and repair. In this study, we conducted different experiments to assess the roles of TopBP1 in DNA repair, mitosis, and meiosis, exploring the relationship between TOPII activity and TopBP1. We found that topbp1 mutant seedlings of Arabidopsis thaliana were hypersensitive to cisplatin treatment and the inhibition of TOPII with etoposide produced similar hypersensitivity levels. Furthermore, we recognised that there were no significant differences between the WT and topbp1 seedlings treated with cisplatin and etoposide together, suggesting that the hypersensitivity to cisplatin in the topbp1 mutant could be related to the functional interaction between TOPII and TopBP1. Somatic and meiotic anaphase bridges appeared in the topbp1 mutant at similar frequencies to those when TOPII was inhibited with merbarone, etoposide, or ICFR-187. The effects on meiosis of TOPII inhibition were produced at S phase/G2 stage, suggesting that catenanes could be produced at the onset of meiosis. Thus, if the processing of the catenanes is impaired, some anaphase bridges can be formed. Also, the appearance of anaphase bridges at first and second division is discussed.
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21
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Dougherty A, Hawaz MG, Hoang KG, Trac J, Keck JM, Ayes C, Deweese JE. Exploration of the Role of the C-Terminal Domain of Human DNA Topoisomerase IIα in Catalytic Activity. ACS OMEGA 2021; 6:25892-25903. [PMID: 34660952 PMCID: PMC8515377 DOI: 10.1021/acsomega.1c02083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Human topoisomerase IIα (TOP2A) is a vital nuclear enzyme involved in resolving knots and tangles in DNA during replication and cell division. TOP2A is a homodimer with a symmetrical, multidomain structure. While the N-terminal and core regions of the protein are well-studied, the C-terminal domain is poorly understood but is involved in enzyme regulation and is predicted to be intrinsically disordered. In addition, it appears to be a major region of post-translational modification and includes several Ser and Thr residues, many of which have not been studied for biochemical effects. Therefore, we generated a series of human TOP2A mutants where we changed specific Ser and Thr residues in the C-terminal domain to Ala, Gly, or Ile residues. We designed, purified, and examined 11 mutant TOP2A enzymes. The amino acid changes were made between positions 1272 and 1525 with 1-7 residues changed per mutant. Several mutants displayed increased levels of DNA cleavage without displaying any change in plasmid DNA relaxation or DNA binding. For example, mutations in the regions 1272-1279, 1324-1343, 1351-1365, and 1374-1377 produced 2-3 times more DNA cleavage in the presence of etoposide than wild-type TOP2A. Further, several mutants displayed changes in relaxation and/or decatenation activity. Together, these results support previous findings that the C-terminal domain of TOP2A influences catalytic activity and interacts with the substrate DNA. Furthermore, we hypothesize that it may be possible to regulate the enzyme by targeting positions in the C-terminal domain. Because the C-terminal domain differs between the two human TOP2 isoforms, this strategy may provide a means for selectively targeting TOP2A for therapeutic inhibition. Additional studies are warranted to explore these results in more detail.
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Affiliation(s)
- Ashley
C. Dougherty
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Mariam G. Hawaz
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Kristine G. Hoang
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Judy Trac
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Jacob M. Keck
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Carmen Ayes
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Joseph E. Deweese
- Department
of Pharmaceutical Sciences, Lipscomb University
College of Pharmacy and Health Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
- Department
of Biochemistry, Vanderbilt University School
of Medicine, 2215 Garland
Avenue, Nashville, Tennessee 37232-0146, United States
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22
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Radaeva M, Ton AT, Hsing M, Ban F, Cherkasov A. Drugging the 'undruggable'. Therapeutic targeting of protein-DNA interactions with the use of computer-aided drug discovery methods. Drug Discov Today 2021; 26:2660-2679. [PMID: 34332092 DOI: 10.1016/j.drudis.2021.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 02/09/2023]
Abstract
Transcription factors (TFs) act as major oncodrivers in many cancers and are frequently regarded as high-value therapeutic targets. The functionality of TFs relies on direct protein-DNA interactions, which are notoriously difficult to target with small molecules. However, this prior view of the 'undruggability' of protein-DNA interfaces has shifted substantially in recent years, in part because of significant advances in computer-aided drug discovery (CADD). In this review, we highlight recent examples of successful CADD campaigns resulting in drug candidates that directly interfere with protein-DNA interactions of several key cancer TFs, including androgen receptor (AR), ETS-related gene (ERG), MYC, thymocyte selection-associated high mobility group box protein (TOX), topoisomerase II (TOP2), and signal transducer and activator of transcription 3 (STAT3). Importantly, these findings open novel and compelling avenues for therapeutic targeting of over 1600 human TFs implicated in many conditions including and beyond cancer.
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Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Michael Hsing
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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23
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Matias-Barrios VM, Radaeva M, Ho CH, Lee J, Adomat H, Lallous N, Cherkasov A, Dong X. Optimization of New Catalytic Topoisomerase II Inhibitors as an Anti-Cancer Therapy. Cancers (Basel) 2021; 13:cancers13153675. [PMID: 34359577 PMCID: PMC8345109 DOI: 10.3390/cancers13153675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary DNA topoisomerase II (TOP2) is a drug target for many types of cancers. However, clinically used TOP2 inhibitors not only kill cancer cells, but also damage normal cells, and can even give rise to other types of cancers. To discover new TOP2 inhibitors to more effectively treat cancer patients, we have applied computer-aided drug design technology to develop several TOP2 inhibitors that can strongly inhibit cancer cell growth but exert low side effects. Results of one exemplary compound are presented in this study. It shows several promising drug-like properties that can be potentially developed into anticancer drugs. Abstract Clinically used topoisomerase II (TOP2) inhibitors are poison inhibitors that induce DNA damage to cause cancer cell death. However, they can also destroy benign cells and thereby show serious side effects, including cardiotoxicity and drug-induced secondary malignancy. New TOP2 inhibitors with a different mechanism of action (MOA), such as catalytic TOP2 inhibitors, are needed to more effectively control tumor growth. We have applied computer-aided drug design to develop a new group of small molecule inhibitors that are derivatives of our previously identified lead compound T60. Particularly, the compound T638 has shown improved solubility and microsomal stability. It is a catalytic TOP2 inhibitor that potently suppresses TOP2 activity. T638 has a novel MOA by which it binds TOP2 proteins and blocks TOP2–DNA interaction. T638 strongly inhibits cancer cell growth, but exhibits limited genotoxicity to cells. These results indicate that T638 is a promising drug candidate that warrants further development into clinically used anticancer drugs.
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Affiliation(s)
| | | | | | | | | | | | | | - Xuesen Dong
- Correspondence: ; Tel.: +1-(604)-875-4111; Fax: +1-(604)-875-5654
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24
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Vann KR, Oviatt AA, Osheroff N. Topoisomerase II Poisons: Converting Essential Enzymes into Molecular Scissors. Biochemistry 2021; 60:1630-1641. [PMID: 34008964 PMCID: PMC8209676 DOI: 10.1021/acs.biochem.1c00240] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The extensive length, compaction, and interwound nature of DNA, together with its controlled and restricted movement in eukaryotic cells, create a number of topological issues that profoundly affect all of the functions of the genetic material. Topoisomerases are essential enzymes that modulate the topological structure of the double helix, including the regulation of DNA under- and overwinding and the removal of tangles and knots from the genome. Type II topoisomerases alter DNA topology by generating a transient double-stranded break in one DNA segment and allowing another segment to pass through the DNA gate. These enzymes are involved in a number of critical nuclear processes in eukaryotic cells, such as DNA replication, transcription, and recombination, and are required for proper chromosome structure and segregation. However, because type II topoisomerases generate double-stranded breaks in the genetic material, they also are intrinsically dangerous enzymes that have the capacity to fragment the genome. As a result of this dualistic nature, type II topoisomerases are the targets for a number of widely prescribed anticancer drugs. This article will describe the structure and catalytic mechanism of eukaryotic type II topoisomerases and will go on to discuss the actions of topoisomerase II poisons, which are compounds that stabilize DNA breaks generated by the type II enzyme and convert these essential enzymes into "molecular scissors." Topoisomerase II poisons represent a broad range of structural classes and include anticancer drugs, dietary components, and environmental chemicals.
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Affiliation(s)
- Kendra R Vann
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alexandria A Oviatt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Departments of Biochemistry and Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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25
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Abstract
1,2-Naphthoquinone, a secondary metabolite of naphthalene, is an environmental pollutant found in diesel exhaust particles that displays cytotoxic and genotoxic properties. Because many quinones have been shown to act as topoisomerase II poisons, the effects of this compound on DNA cleavage mediated by human topoisomerase IIα and IIβ were examined. The compound increased the levels of double-stranded DNA breaks generated by both enzyme isoforms and did so better than a series of naphthoquinone derivatives. Furthermore, 1,2-naphthoquinone was a more efficacious poison against topoisomerase IIα than IIβ. Topoisomerase II poisons can be classified as interfacial (which interact noncovalently at the enzyme-DNA interface and increase DNA cleavage by blocking ligation) or covalent (which adduct the protein and increase DNA cleavage by closing the N-terminal gate of the enzyme). Therefore, experiments were performed to determine the mechanistic basis for the actions of 1,2-naphthoquinone. In contrast to results with etoposide (an interfacial poison), the activity of 1,2-naphthoquinone against topoisomerase IIα was abrogated in the presence of sulfhydryl and reducing agents. Moreover, the compound inhibited cleavage activity when incubated with the enzyme prior to the addition of DNA and induced virtually no cleavage with the catalytic core of the enzyme. It also induced stable covalent topoisomerase IIα-DNA cleavage complexes and was a partial inhibitor of DNA ligation. Findings were also consistent with 1,2-naphthoquinone acting as a covalent poison of topoisomerase IIβ; however, mechanistic studies with this isoform were less conclusive. Whereas the activity of 1,2-naphthoquinone was blocked in the presence of a sulfhydryl reagent, it was much less sensitive to the presence of a reducing agent. Furthermore, the reduced form of 1,2-naphthoquinone, 1,2-dihydroxynaphthalene, displayed high activity against the β isoform. Taken together, results suggest that 1,2-naphthoquinone increases topoisomerase II-mediated double-stranded DNA scission (at least in part) by acting as a covalent poison of the human type II enzymes.
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Affiliation(s)
- Jessica A. Collins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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26
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Herrero-Ruiz A, Martínez-García PM, Terrón-Bautista J, Millán-Zambrano G, Lieberman JA, Jimeno-González S, Cortés-Ledesma F. Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing. Cell Rep 2021; 35:108977. [PMID: 33852840 PMCID: PMC8052185 DOI: 10.1016/j.celrep.2021.108977] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 02/05/2021] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
Accumulation of topological stress in the form of DNA supercoiling is inherent to the advance of RNA polymerase II (Pol II) and needs to be resolved by DNA topoisomerases to sustain productive transcriptional elongation. Topoisomerases are therefore considered positive facilitators of transcription. Here, we show that, in contrast to this general assumption, human topoisomerase IIα (TOP2A) activity at promoters represses transcription of immediate early genes such as c-FOS, maintaining them under basal repressed conditions. Thus, TOP2A inhibition creates a particular topological context that results in rapid release from promoter-proximal pausing and transcriptional upregulation, which mimics the typical bursting behavior of these genes in response to physiological stimulus. We therefore describe the control of promoter-proximal pausing by TOP2A as a layer for the regulation of gene expression, which can act as a molecular switch to rapidly activate transcription, possibly by regulating the accumulation of DNA supercoiling at promoter regions.
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Affiliation(s)
- Andrés Herrero-Ruiz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - José Terrón-Bautista
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | | | - Silvia Jimeno-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain.
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain.
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27
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Matias-Barrios VM, Radaeva M, Song Y, Alperstein Z, Lee AR, Schmitt V, Lee J, Ban F, Xie N, Qi J, Lallous N, Gleave ME, Cherkasov A, Dong X. Discovery of New Catalytic Topoisomerase II Inhibitors for Anticancer Therapeutics. Front Oncol 2021; 10:633142. [PMID: 33598437 PMCID: PMC7883873 DOI: 10.3389/fonc.2020.633142] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/15/2020] [Indexed: 01/23/2023] Open
Abstract
Poison inhibitors of DNA topoisomerase II (TOP2) are clinically used drugs that cause cancer cell death by inducing DNA damage, which mechanism of action is also associated with serious side effects such as secondary malignancy and cardiotoxicity. In contrast, TOP2 catalytic inhibitors induce limited DNA damage, have low cytotoxicity, and are effective in suppressing cancer cell proliferation. They have been sought after to be prospective anticancer therapies. Herein the discovery of new TOP2 catalytic inhibitors is described. A new druggable pocket of TOP2 protein at its DNA binding domain was used as a docking site to virtually screen ~6 million molecules from the ZINC15 library. The lead compound, T60, was characterized to be a catalytic TOP2 inhibitor that binds TOP2 protein and disrupts TOP2 from interacting with DNA, resulting in no DNA cleavage. It has low cytotoxicity, but strongly inhibits cancer cell proliferation and xenograft growth. T60 also inhibits androgen receptor activity and prostate cancer cell growth. These results indicate that T60 is a promising candidate compound that can be further developed into new anticancer drugs.
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Affiliation(s)
- Victor M Matias-Barrios
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Mariia Radaeva
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yi Song
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zaccary Alperstein
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ahn R Lee
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Veronika Schmitt
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Joseph Lee
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Fuqiang Ban
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ning Xie
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Nada Lallous
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin E Gleave
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Artem Cherkasov
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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28
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Cetin R, Quandt E, Kaulich M. Functional Genomics Approaches to Elucidate Vulnerabilities of Intrinsic and Acquired Chemotherapy Resistance. Cells 2021; 10:cells10020260. [PMID: 33525637 PMCID: PMC7912423 DOI: 10.3390/cells10020260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Drug resistance is a commonly unavoidable consequence of cancer treatment that results in therapy failure and disease relapse. Intrinsic (pre-existing) or acquired resistance mechanisms can be drug-specific or be applicable to multiple drugs, resulting in multidrug resistance. The presence of drug resistance is, however, tightly coupled to changes in cellular homeostasis, which can lead to resistance-coupled vulnerabilities. Unbiased gene perturbations through RNAi and CRISPR technologies are invaluable tools to establish genotype-to-phenotype relationships at the genome scale. Moreover, their application to cancer cell lines can uncover new vulnerabilities that are associated with resistance mechanisms. Here, we discuss targeted and unbiased RNAi and CRISPR efforts in the discovery of drug resistance mechanisms by focusing on first-in-line chemotherapy and their enforced vulnerabilities, and we present a view forward on which measures should be taken to accelerate their clinical translation.
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Affiliation(s)
- Ronay Cetin
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
| | - Eva Quandt
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Barcelona, Spain;
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)-69-6301-5450
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29
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Bicyclic Basic Merbarone Analogues as Antiproliferative Agents. Molecules 2021; 26:molecules26030557. [PMID: 33494519 PMCID: PMC7866144 DOI: 10.3390/molecules26030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Pyrimido-pyrimidine derivatives have been developed as rigid merbarone analogues. In a previous study, these compounds showed potent antiproliferative activity and efficiently inhibited topoisomerase IIα. To further extend the structure-activity relationships on pyrimido-pyrimidines, a novel series of analogues was synthesized by a two-step procedure. Analogues 3-6 bear small alky groups at positions 1 and 3 of the pyrimido-pyrimidine scaffold whereas at position 6a (4-chloro)phenyl substituent was inserted. The basic side chains introduced at position 7 were selected on the basis of the previously developed structure-activity relationships. The antiproliferative activity of the novel compounds proved to be affected by both the nature of the basic side chain and the substituents on the pyrimido-pyrimidine moiety. Derivatives 5d and 5e were identified as the most promising molecules still showing reduced antiproliferative activity in comparison with the previously prepared pyrimido-pyrimidine analogues. In topoisomerase IIα-5d docking complex, the ligand would poorly interact with the enzyme and assume a different orientation in comparison with 1d bioactive conformation.
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30
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Buzun K, Bielawska A, Bielawski K, Gornowicz A. DNA topoisomerases as molecular targets for anticancer drugs. J Enzyme Inhib Med Chem 2020; 35:1781-1799. [PMID: 32975138 PMCID: PMC7534307 DOI: 10.1080/14756366.2020.1821676] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023] Open
Abstract
The significant role of topoisomerases in the control of DNA chain topology has been confirmed in numerous research conducted worldwide. The prevalence of these enzymes, as well as the key importance of topoisomerase in the proper functioning of cells, have made them the target of many scientific studies conducted all over the world. This article is a comprehensive review of knowledge about topoisomerases and their inhibitors collected over the years. Studies on the structure-activity relationship and molecular docking are one of the key elements driving drug development. In addition to information on molecular targets, this article contains details on the structure-activity relationship of described classes of compounds. Moreover, the work also includes details about the structure of the compounds that drive the mode of action of topoisomerase inhibitors. Finally, selected topoisomerases inhibitors at the stage of clinical trials and their potential application in the chemotherapy of various cancers are described.
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Affiliation(s)
- Kamila Buzun
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Bielawska
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Bialystok, Poland
| | - Agnieszka Gornowicz
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
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31
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de Souza Pereira C, Costa Quadros H, Magalhaes Moreira DR, Castro W, Santos De Deus Da Silva RI, Botelho Pereira Soares M, Fontinha D, Prudêncio M, Schmitz V, Dos Santos HF, Gendrot M, Fonta I, Mosnier J, Pradines B, Navarro M. A Novel Hybrid of Chloroquine and Primaquine Linked by Gold(I): Multitarget and Multiphase Antiplasmodial Agent. ChemMedChem 2020; 16:662-678. [PMID: 33231370 DOI: 10.1002/cmdc.202000653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/02/2020] [Indexed: 12/23/2022]
Abstract
Plasmodium parasites kill 435 000 people around the world every year due to unavailable vaccines, a limited arsenal of antimalarial drugs, delayed treatment, and the reduced clinical effectiveness of current practices caused by drug resistance. Therefore, there is an urgent need to discover and develop new antiplasmodial candidates. In this work, we present a novel strategy to develop a multitarget metallic hybrid antimalarial agent with possible dual efficacy in both sexual and asexual erythrocytic stages. A hybrid of antimalarial drugs (chloroquine and primaquine) linked by gold(I) was synthesized and characterized by spectroscopic and analytical techniques. The CQPQ-gold(I) hybrid molecule affects essential parasite targets, it inhibits β-hematin formation and interacts moderately with the DNA minor groove. Its interaction with PfTrxR was also examined in computational modeling studies. The CQPQ-gold(I) hybrid displayed an excellent in vitro antimalarial activity against the blood-stage of Plasmodium falciparum and liver-stage of Plasmodium berghei and efficacy in vivo against P. berghei, thereby demonstrating its multiple-stage antiplasmodial activity. This metallic hybrid is a promising chemotherapeutic agent that could act in the treatment, prevention, and transmission of malaria.
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Affiliation(s)
- Caroline de Souza Pereira
- Departamento de Química, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro Martelos, CEP 36036-900, Juiz de Fora, Minas Gerais, Brasil
| | - Helenita Costa Quadros
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Av. Waldemar Falcão, 121, Candeal, Salvador, Bahia, Brasil
| | | | - William Castro
- Centro de Química, Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Química, Carretera Panamericana, Km 11, Altos de Pipe, San Antonio de los Altos Miranda, 1020-A, Caracas, Venezuela
| | | | | | - Diana Fontinha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa <, Lisboa, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa <, Lisboa, Portugal
| | - Vinicius Schmitz
- Departamento de Química, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro Martelos, CEP 36036-900, Juiz de Fora, Minas Gerais, Brasil
| | - Hélio F Dos Santos
- Departamento de Química, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro Martelos, CEP 36036-900, Juiz de Fora, Minas Gerais, Brasil
| | - Mathieu Gendrot
- Unité Parasitologie et entomologie, Institut de recherche biomédicale des armées, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ, IRD, SSA, AP-HM, VITROME, 19-21 Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et entomologie, Institut de recherche biomédicale des armées, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ, IRD, SSA, AP-HM, VITROME, 19-21 Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Centre National de Référence du Paludisme, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et entomologie, Institut de recherche biomédicale des armées, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ, IRD, SSA, AP-HM, VITROME, 19-21 Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Centre National de Référence du Paludisme, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et entomologie, Institut de recherche biomédicale des armées, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ, IRD, SSA, AP-HM, VITROME, 19-21 Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Centre National de Référence du Paludisme, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Maribel Navarro
- Departamento de Química, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro Martelos, CEP 36036-900, Juiz de Fora, Minas Gerais, Brasil
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32
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Ortega JA, Arencibia JM, Minniti E, Byl JAW, Franco-Ulloa S, Borgogno M, Genna V, Summa M, Bertozzi SM, Bertorelli R, Armirotti A, Minarini A, Sissi C, Osheroff N, De Vivo M. Novel, Potent, and Druglike Tetrahydroquinazoline Inhibitor That Is Highly Selective for Human Topoisomerase II α over β. J Med Chem 2020; 63:12873-12886. [PMID: 33079544 PMCID: PMC7668297 DOI: 10.1021/acs.jmedchem.0c00774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
We disclose a novel
class of 6-amino-tetrahydroquinazoline derivatives
that inhibit human topoisomerase II (topoII), a validated target of
anticancer drugs. In contrast to topoII-targeted drugs currently in
clinical use, these compounds do not act as topoII poisons that enhance
enzyme-mediated DNA cleavage, a mechanism that is linked to the development
of secondary leukemias. Instead, these tetrahydroquinazolines block
the topoII function with no evidence of DNA intercalation. We identified
a potent lead compound [compound 14 (ARN-21934) IC50 = 2 μM for inhibition of DNA relaxation, as compared
to an IC50 = 120 μM for the anticancer drug etoposide]
with excellent metabolic stability and solubility. This new compound
also shows ~100-fold selectivity for topoIIα over topoβ,
a broad antiproliferative activity toward cultured human cancer cells,
a favorable in vivo pharmacokinetic profile, and the ability to penetrate
the blood–brain barrier. Thus, ARN-21934 is a highly promising
lead for the development of novel and potentially safer topoII-targeted
anticancer drugs.
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Affiliation(s)
- Jose Antonio Ortega
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jose M Arencibia
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Elirosa Minniti
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.,Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Sebastian Franco-Ulloa
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marco Borgogno
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Maria Summa
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry & Translational Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Anna Minarini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6307, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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33
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Murphy MB, Kumar P, Bradley AM, Barton CE, Deweese JE, Mercer SL. Synthesis and evaluation of etoposide and podophyllotoxin analogs against topoisomerase IIα and HCT-116 cells. Bioorg Med Chem 2020; 28:115773. [PMID: 33035756 DOI: 10.1016/j.bmc.2020.115773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022]
Abstract
Etoposide is a widely-used anticancer agent that targets human type II topoisomerases. Evidence suggests that metabolism of etoposide in myeloid progenitor cells is associated with translocations involved in leukemia development. Previous studies suggest halogenation at the C-2' position of etoposide reduces metabolism. Halogens were introduced into the C-2' position by electrophilic aromatic halogenation onto etoposide (ETOP, 1), podophyllotoxin (PPT, 2), and 4-dimethylepipodophyllotoxin (DMEP, 3), and to bridge the gap of knowledge regarding the activity of these metabolically stable analogs. Five halogenated analogs (6-10) were synthesized. Analogs 8-10 displayed variable ability to inhibit DNA relaxation. Analog 9 was the only analog to show concentration-dependent enhancement of Top2-mediated DNA cleavage. Dose response assay results indicated that 8 and 10 were most effective at decreasing the viability of HCT-116 and A549 cancer cell lines in culture. Flow cytometry with 8 and 10 in HCT-116 cells provide evidence of sub-G1 cell populations indicative of apoptosis. Taken together, these results indicate C-2' halogenation of etoposide and its precursors, although metabolically stable, decreases overall activity relative to etoposide.
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Affiliation(s)
- Matthew B Murphy
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, One University, Park Drive, Nashville, TN 37204, USA
| | - Priyanka Kumar
- Department of Biology, Belmont University, 1900 Belmont Boulevard, Nashville, TN 37212, USA
| | - Amber M Bradley
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, One University, Park Drive, Nashville, TN 37204, USA
| | - Christopher E Barton
- Department of Biology, Belmont University, 1900 Belmont Boulevard, Nashville, TN 37212, USA
| | - Joseph E Deweese
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, One University, Park Drive, Nashville, TN 37204, USA; Departments of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Susan L Mercer
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, One University, Park Drive, Nashville, TN 37204, USA; Departments of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA.
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34
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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35
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Bergant Loboda K, Janežič M, Štampar M, Žegura B, Filipič M, Perdih A. Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα. J Chem Inf Model 2020; 60:3662-3678. [PMID: 32484690 PMCID: PMC7469689 DOI: 10.1021/acs.jcim.0c00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class of substituted 4,5'-bithiazoles as catalytic inhibitors targeting the human DNA topoisomerase IIα. Based on a structural comparison of the ATPase domains of human and bacterial type II topoisomerase, a focused chemical library of 4,5'-bithiazoles was assembled and screened to identify compounds that better fit the topology of the human topo IIα adenosine 5'-triphosphate (ATP) binding site. Selected compounds showed inhibition of human topo IIα comparable to that of the etoposide topo II drug, revealing a new class of inhibitors targeting this molecular motor. Further investigations showed that compounds act as catalytic inhibitors via competitive ATP inhibition. We also confirmed binding to the truncated ATPase domain of topo IIα and modeled the inhibitor molecular recognition with molecular simulations and dynophore models. The compounds also displayed promising cytotoxicity against HepG2 and MCF-7 cell lines comparable to that of etoposide. In a more detailed study with the HepG2 cell line, there was no induction of DNA double-strand breaks (DSBs), and the compounds were able to reduce cell proliferation and stop the cell cycle mainly in the G1 phase. This confirms the mechanism of action of these compounds, which differs from topo II poisons also at the cellular level. Substituted 4,5'-bithiazoles appear to be a promising class for further development toward efficient and potentially safer cancer therapies exploiting the alternative topo II inhibition paradigm.
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Affiliation(s)
- Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matej Janežič
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Martina Štampar
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Metka Filipič
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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36
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Design and synthesis of 3,5-substituted 1,2,4-oxadiazoles as catalytic inhibitors of human DNA topoisomerase IIα. Bioorg Chem 2020; 99:103828. [DOI: 10.1016/j.bioorg.2020.103828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/20/2020] [Accepted: 04/05/2020] [Indexed: 01/05/2023]
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37
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Arencibia JM, Brindani N, Franco-Ulloa S, Nigro M, Kuriappan JA, Ottonello G, Bertozzi SM, Summa M, Girotto S, Bertorelli R, Armirotti A, De Vivo M. Design, Synthesis, Dynamic Docking, Biochemical Characterization, and in Vivo Pharmacokinetics Studies of Novel Topoisomerase II Poisons with Promising Antiproliferative Activity. J Med Chem 2020; 63:3508-3521. [PMID: 32196342 PMCID: PMC7997578 DOI: 10.1021/acs.jmedchem.9b01760] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
We
previously reported a first set of hybrid topoisomerase II (topoII)
poisons whose chemical core merges key pharmacophoric elements of
etoposide and merbarone, which are two well-known topoII blockers.
Here, we report on the expansion of this hybrid molecular scaffold
and present 16 more hybrid derivatives that have been designed, synthesized,
and characterized for their ability to block topoII and for their
overall drug-like profile. Some of these compounds act as topoII poison
and exhibit good solubility, metabolic (microsomal) stability, and
promising cytotoxicity in three cancer cell lines (DU145, HeLa, A549).
Compound 3f (ARN24139) is the most promising drug-like
candidate, with a good pharmacokinetics profile in vivo. Our results indicate that this hybrid new chemical class of topoII
poisons deserves further exploration and that 3f is a
favorable lead candidate as a topoII poison, meriting future studies
to test its efficacy in in vivo tumor models.
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Affiliation(s)
- Jose M Arencibia
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sebastian Franco-Ulloa
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Michela Nigro
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Giuliana Ottonello
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sine Mandrup Bertozzi
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Maria Summa
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Stefania Girotto
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Rosalia Bertorelli
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- Analytical Chemistry and in Vivo Pharmacology, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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Pedatella S, Cerchia C, Manfra M, Cioce A, Bolognese A, Lavecchia A. Antitumor agents 7. Synthesis, antiproliferative activity and molecular modeling of new l-lysine-conjugated pyridophenoxazinones as potent DNA-binding ligands and topoisomerase IIα inhibitors. Eur J Med Chem 2019; 187:111960. [PMID: 31869654 DOI: 10.1016/j.ejmech.2019.111960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/20/2019] [Accepted: 12/09/2019] [Indexed: 01/24/2023]
Abstract
A series of l-lysine-conjugated pyridophenoxazinones 2-5 and 2'-5' were designed and synthesized for developing compounds with multimodal anticancer potentialities. All compounds inhibited the proliferation of a panel of human liquid and solid neoplastic cell lines. 2 and 5 were the most active compounds with IC50 values in the submicromolar range. UV-vis, 1H NMR, unwinding, and docking experiments demonstrated that they intercalate between the middle 5'-GC-3' base pairs with the carboxamide side chain lying into major groove. Charge-transfer contribution to the complex stability, evaluated by ab initio calculations, was found to correlate with cytotoxicity. Relaxation and cleavage assays showed that 2 and 5 selectively target Topo IIα over Topo IIβ and stimulate the formation of covalent Topo II-DNA complexes, functioning as poisons. Moreover, compound 5 induced DNA damage and arrested MCF-7 cells at the G2/M phase. Altogether, the work provides interesting structure-activity relationships in the pyridophenoxazinone-l-lysine conjugate series and identifies 5 as a promising candidate for further in vivo evaluation.
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Affiliation(s)
- Silvana Pedatella
- Department of Chemical Sciences, University of Naples Federico II, via Cynthia 6, Monte Sant'Angelo, 80126, Naples, Italy
| | - Carmen Cerchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Michele Manfra
- Department of Science, University of Basilicata, viale dell'Ateneo Lucano 10, 85100, Potenza, Italy.
| | - Anna Cioce
- Department of Glycotechnology, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Spain
| | - Adele Bolognese
- Department of Chemical Sciences, University of Naples Federico II, via Cynthia 6, Monte Sant'Angelo, 80126, Naples, Italy
| | - Antonio Lavecchia
- Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy.
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39
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Benzoxazines as new human topoisomerase I inhibitors and potential poisons. ACTA ACUST UNITED AC 2019; 28:65-73. [PMID: 31832989 DOI: 10.1007/s40199-019-00315-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 11/13/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND The numbers of topoisomerase I targeted drugs on the market are very limited although they are used clinically for treatment of solid tumors. Hence, studies about finding new chemical structures which specifically target topoisomerase I are still remarkable. OBJECTIVES In this present study, we tested previously synthesized 3,4-dihydro-2H-1,4-benzoxazin-3-one derivatives to reveal their human DNA topoisomerase I inhibitory potentials. METHODS We investigated inhibitory activities of 3,4-dihydro-2H-1,4-benzoxazin-3-one derivatives on human topoisomerase I by relaxation assay to clarify inhibition mechanisms of effective derivatives with EMSA and T4 DNA ligase based intercalation assay. With SAR study, it was tried to find out effective groups in the ring system. RESULTS While 10 compounds showed catalytic inhibitory activity, 8 compounds were found to be potential topoisomerase poisons. 4 of them also exhibited both activities. 2-hydroxy-3,4-dihydro-2H-1,4-benzoxazin-3-one (BONC-001) was the most effective catalytic inhibitor (IC50:8.34 mM) and ethyl 6-chloro-4-methyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-acetate (BONC-013) was the strongest potential poison (IC50:0.0006 mM). BONC-013 was much more poisonous than camptothecin (IC50:0.034 mM). Intercalation assay showed that BONC-013 was not an intercalator and BONC-001 most probably prevented enzyme-substrate binding in an unknown way. Another important result of this study was that OH group instead of ethoxycarbonylmethyl group at R position of benzoxazine ring was important for hTopo I catalytic inhibition while the attachment of a methyl group of R1 position at R2 position were play a role for increasing of its poisonous effect. CONCLUSION As a result, we presented new DNA topoisomerase I inhibitors which might serve novel constructs for future anticancer agent designs. Graphical abstract.
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40
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Atkin ND, Raimer HM, Wang YH. Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility. Genes (Basel) 2019; 10:E791. [PMID: 31614754 PMCID: PMC6826763 DOI: 10.3390/genes10100791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/05/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
DNA topoisomerase II (TOP2) plays a critical role in many processes such as replication and transcription, where it resolves DNA structures and relieves torsional stress. Recent evidence demonstrated the association of TOP2 with topologically associated domains (TAD) boundaries and CCCTC-binding factor (CTCF) binding sites. At these sites, TOP2 promotes interactions between enhancers and gene promoters, and relieves torsional stress that accumulates at these physical barriers. Interestingly, in executing its enzymatic function, TOP2 contributes to DNA fragility through re-ligation failure, which results in persistent DNA breaks when unrepaired or illegitimately repaired. Here, we discuss the biological processes for which TOP2 is required and the steps at which it can introduce DNA breaks. We describe the repair processes that follow removal of TOP2 adducts and the resultant broken DNA ends, and present how these processes can contribute to disease-associated mutations. Furthermore, we examine the involvement of TOP2-induced breaks in the formation of oncogenic translocations of leukemia and papillary thyroid cancer, as well as the role of TOP2 and proteins which repair TOP2 adducts in other diseases. The participation of TOP2 in generating persistent DNA breaks and leading to diseases such as cancer, could have an impact on disease treatment and prevention.
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Affiliation(s)
- Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.
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41
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Keck JM, Conner JD, Wilson JT, Jiang X, Lisic EC, Deweese JE. Clarifying the Mechanism of Copper(II) α-(N)-Heterocyclic Thiosemicarbazone Complexes on DNA Topoisomerase IIα and IIβ. Chem Res Toxicol 2019; 32:2135-2143. [PMID: 31512855 DOI: 10.1021/acs.chemrestox.9b00311] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Topoisomerase II is a nuclear enzyme involved in the maintenance of DNA and is an effective anticancer drug target. However, several clinical topoisomerase II-targeted agents display significant off-target toxicities and adverse events. Thus, it is important to continue characterizing compounds with activity against topoisomerase II. We previously analyzed α-(N)-heterocyclic thiosemicarbazone copper(II) complexes against human topoisomerase IIα (TOP2A), but humans also express topoisomerase IIβ (TOP2B), which has distinct functional roles. Therefore, we examined two α-(N)-heterocyclic thiosemicarbazone copper [Cu(II)] complexes for activity against TOP2B in a purified system. The Cu(II) complexes, Cu(APY-ETSC)Cl and Cu(BZP-ETSC)Cl, were examined using plasmid DNA cleavage, supercoiled DNA relaxation, enzyme inactivation, protein cross-linking, DNA ligation, and ATP hydrolysis assays with TOP2B to determine whether these compounds act similarly against both enzymes. Both of the Cu(II) thiosemicarbazone (Cu-TSC) complexes we tested disrupted the function of TOP2B in a way similar to the effect on TOP2A. In particular, TOP2B DNA cleavage activity is increased in the presence of these compounds, while the relaxation and ATPase activities are inhibited. Further, both Cu-TSCs stabilize the N-terminal DNA clamp of TOP2A and TOP2B and rapidly inactivate TOP2B when the compounds are present before DNA. Our data provide evidence that the Cu-TSC complexes we tested utilize a similar mechanism against both isoforms of the enzyme. This mechanism may involve interaction with the ATPase domain of TOP2A and TOP2B outside of the ATP binding pocket. Additionally, these data support a model of TOP2 function where the ATPase domain communicates with the DNA cleavage/ligation domain.
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Affiliation(s)
- J Myles Keck
- Department of Pharmaceutical Sciences , Lipscomb University College of Pharmacy and Health Sciences , Nashville , Tennessee 37204-3951 , United States
| | - Jennifer D Conner
- Department of Chemistry , Tennessee Technological University , Cookeville , Tennessee 38505 , United States
| | - James T Wilson
- Department of Pharmaceutical Sciences , Lipscomb University College of Pharmacy and Health Sciences , Nashville , Tennessee 37204-3951 , United States
| | - Xiaohua Jiang
- Department of Chemistry , Tennessee Technological University , Cookeville , Tennessee 38505 , United States
| | - Edward C Lisic
- Department of Chemistry , Tennessee Technological University , Cookeville , Tennessee 38505 , United States
| | - Joseph E Deweese
- Department of Pharmaceutical Sciences , Lipscomb University College of Pharmacy and Health Sciences , Nashville , Tennessee 37204-3951 , United States.,Department of Biochemistry , Vanderbilt University School of Medicine , Nashville , Tennessee 37232-0146 , United States
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42
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Ahmed SM, Dröge P. Oncofetal HMGA2 attenuates genotoxic damage induced by topoisomerase II target compounds through the regulation of local DNA topology. Mol Oncol 2019; 13:2062-2078. [PMID: 31271486 PMCID: PMC6763970 DOI: 10.1002/1878-0261.12541] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/26/2022] Open
Abstract
Rapidly dividing cells maintain chromatin supercoiling homeostasis via two specialized classes of enzymes, DNA topoisomerase type 1 and 2 (TOP1/2). Several important anticancer drugs perturb this homeostasis by targeting TOP1/2, thereby generating genotoxic DNA damage. Our recent studies indicated that the oncofetal chromatin structuring high‐mobility group AT‐hook 2 (HMGA2) protein plays an important role as a DNA replication fork chaperone in coping with DNA topological ramifications that occur during replication stress, both genomewide and at fragile sites such as subtelomeres. Intriguingly, a recent large‐scale clinical study identified HMGA2 expression as a sole predicting marker for relapse and poor clinical outcomes in 350 acute myeloid leukemia (AML) patients receiving combinatorial treatments that targeted TOP2 and replicative DNA synthesis. Here, we demonstrate that HMGA2 significantly enhanced the DNA supercoil relaxation activity of the drug target TOP2A and that this activator function is mechanistically linked to HMGA2's known ability to constrain DNA supercoils within highly compacted ternary complexes. Furthermore, we show that HMGA2 significantly reduced genotoxic DNA damage in each tested cancer cell model during treatment with the TOP2A poison etoposide or the catalytic TOP2A inhibitor merbarone. Taken together with the recent clinical data obtained with AML patients targeted with TOP2 poisons, our study suggests a novel mechanism of cancer chemoresistance toward combination therapies administering TOP2 poisons or inhibitors. We therefore strongly argue for the future implementation of trials of HMGA2 expression profiling to stratify patients before finalizing clinical treatment regimes.
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Affiliation(s)
- Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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43
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Rocha FV, Farias RL, Lima MA, Batista VS, Nascimento-Júnior NM, Garrido SS, Leopoldino AM, Goto RN, Oliveira AB, Beck J, Landvogt C, Mauro AE, Netto AVG. Computational studies, design and synthesis of Pd(II)-based complexes: Allosteric inhibitors of the Human Topoisomerase-IIα. J Inorg Biochem 2019; 199:110725. [PMID: 31374424 DOI: 10.1016/j.jinorgbio.2019.110725] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022]
Abstract
Herein, a robust docking protocol was developed by using a low-cost workflow to highlight the modulation at ATPase domain from Human Topoisomerase-IIα (TOP2A) towards four novel Pd(II)-complexes bearing N,S-donor ligands. In vitro TOP2A inhibition assay confirmed the ability of them to prevent the enzyme functions into concentration ranging at 6.25-25μM. These results exhibited more effectivity than anticancer agent etoposide (35μM) and merbarone (40-50μM). The compounds were screened via Resazurin assay against MCF-7, MDA-MB-231 (Human breast), DU-145 (Human prostate), A549 (Human lung) and Cal27 (Human tongue) tumor cell lines revealing great cytotoxic effects, primarily to MCF-7 (IC50=1.81-4.46μM). As well, 1-4 exhibited their selectivity index (SI) higher than cisplatin against HEK-293 (human kidney) normal cells, at least 11.6-fold (SI1-4=1.4-5.0; SIcis=0.12). Further, Red Blood Cell hemolytic test suggested in vitro non-toxic character for compound 4, previously evaluated as the most effective TOP2A inhibitor.
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Affiliation(s)
- Fillipe V Rocha
- UFSCar - Univ Federal de São Carlos, Departamento de Química, São Carlos, Brazil.
| | - Renan L Farias
- UNESP - Univ Estadual Paulista, Instituto de Química, Departamento de Química Geral e Inorgânica, Araraquara, Brazil
| | - Mauro A Lima
- UFSCar - Univ Federal de São Carlos, Departamento de Química, São Carlos, Brazil
| | - Victor S Batista
- UNESP - Univ Estadual Paulista, Instituto de Química, Departamento de Química Orgânica, Araraquara, Brazil
| | | | - Saulo S Garrido
- UNESP - Univ Estadual Paulista, Instituto de Química, Departamento de Bioquímica e Tecnologia Química, Araraquara, Brazil
| | - Andréia M Leopoldino
- USP - Univ de São Paulo, Department of Clinical Analyses, Toxicology and Food Sciences, Ribeirão Preto, Brazil
| | - Renata N Goto
- USP - Univ de São Paulo, Department of Clinical Analyses, Toxicology and Food Sciences, Ribeirão Preto, Brazil
| | - Adriano B Oliveira
- UFS - Univ Federal de Sergipe, Departamento de Química, São Cristóvão, Brazil
| | - Johannes Beck
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Bonn, Germany
| | - Christian Landvogt
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Bonn, Germany
| | - Antônio E Mauro
- UNESP - Univ Estadual Paulista, Instituto de Química, Departamento de Química Geral e Inorgânica, Araraquara, Brazil
| | - Adelino V G Netto
- UNESP - Univ Estadual Paulista, Instituto de Química, Departamento de Química Geral e Inorgânica, Araraquara, Brazil
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Cellular DNA Topoisomerases Are Required for the Synthesis of Hepatitis B Virus Covalently Closed Circular DNA. J Virol 2019; 93:JVI.02230-18. [PMID: 30867306 DOI: 10.1128/jvi.02230-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/01/2019] [Indexed: 12/18/2022] Open
Abstract
In order to identify host cellular DNA metabolic enzymes that are involved in the biosynthesis of hepatitis B virus (HBV) covalently closed circular (ccc) DNA, we developed a cell-based assay supporting synchronized and rapid cccDNA synthesis from intracellular progeny nucleocapsid DNA. This was achieved by arresting HBV DNA replication in HepAD38 cells with phosphonoformic acid (PFA), a reversible HBV DNA polymerase inhibitor, at the stage of single-stranded DNA and was followed by removal of PFA to allow the synchronized synthesis of relaxed circular DNA (rcDNA) and subsequent conversion into cccDNA within 12 to 24 h. This cccDNA formation assay allows systematic screening of the effects of small molecular inhibitors of DNA metabolic enzymes on cccDNA synthesis but avoids cytotoxic effects upon long-term treatment. Using this assay, we found that all the tested topoisomerase I and II (TOP1 and TOP2, respectively) poisons as well as topoisomerase II DNA binding and ATPase inhibitors significantly reduced the levels of cccDNA. It was further demonstrated that these inhibitors also disrupted cccDNA synthesis during de novo HBV infection of HepG2 cells expressing sodium taurocholate cotransporting polypeptide (NTCP). Mechanistic analyses indicate that whereas TOP1 inhibitor treatment prevented the production of covalently closed negative-strand rcDNA, TOP2 inhibitors reduced the production of this cccDNA synthesis intermediate to a lesser extent. Moreover, small interfering RNA (siRNA) knockdown of topoisomerase II significantly reduced cccDNA amplification. Taking these observations together, our study demonstrates that topoisomerase I and II may catalyze distinct steps of HBV cccDNA synthesis and that pharmacologic targeting of these cellular enzymes may facilitate the cure of chronic hepatitis B.IMPORTANCE Persistent HBV infection relies on stable maintenance and proper functioning of a nuclear episomal form of the viral genome called cccDNA, the most stable HBV replication intermediate. One of the major reasons for the failure of currently available antiviral therapeutics to cure chronic HBV infection is their inability to eradicate or inactivate cccDNA. We report here a chemical genetics approach to identify host cellular factors essential for the biosynthesis and maintenance of cccDNA and reveal that cellular DNA topoisomerases are required for both de novo synthesis and intracellular amplification of cccDNA. This approach is suitable for systematic screening of compounds targeting cellular DNA metabolic enzymes and chromatin remodelers for their ability to disrupt cccDNA biosynthesis and function. Identification of key host factors required for cccDNA metabolism and function will reveal molecular targets for developing curative therapeutics of chronic HBV infection.
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A high-throughput screen of pharmacologically active compounds for inhibitors of UHRF1 reveals epigenetic activity of anthracycline derivative chemotherapeutic drugs. Oncotarget 2019; 10:3040-3050. [PMID: 31105884 PMCID: PMC6508961 DOI: 10.18632/oncotarget.26889] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/11/2019] [Indexed: 01/04/2023] Open
Abstract
DNA methylation can mediate epigenetic silencing of tumor suppressor and cancer protective genes. The protein ubiquitin-like containing PHD and ring finger domains 1 (UHRF1) is an essential component in cells for DNA methylation maintenance. The SET- and RING-associated (SRA) domain of UHRF1 can bind hemimethylated DNA, and mediate recruitment of DNA methyltransferases to copy the methylation pattern to the newly synthesized daughter strand. Loss of UHRF1 function can lead to demethylation and re-expression of epigenetically silenced tumor suppressor genes and can reduce cancer cell growth and survival. We created a high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) assay to screen for inhibitors capable of disrupting the interaction between the UHRF1-SRA domain and hemimethylated DNA. Using this assay (Z' factor of 0.74 in 384-well format) we screened the Library of Pharmacologically Active Compounds (LOPAC) for UHRF1-SRA inhibitors, and validated 7 hit compounds. These compounds included the anthracycline derivatives idarubicin and mitoxantrone, which are commonly used chemotherapeutic drugs known to mediate cytotoxicity by acting as class II topoisomerase (TOP2) poisons. In a panel of additional known topoisomerase poisons, only the anthracycline derivatives showed dose responsive inhibition of UHRF1-SRA. Additionally, mitoxantrone and doxorubicin showed dose-responsive global DNA demethylation and demonstrated a synergistic growth inhibition of multiple cancer cell lines when combined with the DNA methyltransferase (DNMT) inhibitor decitabine. These data validate a novel TR-FRET assay for identification of UHRF1 inhibitors, and revealed unexpected epigenetic properties of commonly used chemotherapeutic drugs that showed synergistic cytotoxicity of cancer cells when combined with a demethylating agent.
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Khalil OM, Gedawy EM, El-Malah AA, Adly ME. Novel nalidixic acid derivatives targeting topoisomerase II enzyme; Design, synthesis, anticancer activity and effect on cell cycle profile. Bioorg Chem 2019; 83:262-276. [DOI: 10.1016/j.bioorg.2018.10.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 10/28/2022]
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El-Zahabi HS, Khalifa MM, Gado YM, Farrag AM, Elaasser MM, Safwat NA, AbdelRaouf RR, Arafa RK. New thiobarbituric acid scaffold-based small molecules: Synthesis, cytotoxicity, 2D-QSAR, pharmacophore modelling and in-silico ADME screening. Eur J Pharm Sci 2019; 130:124-136. [DOI: 10.1016/j.ejps.2019.01.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/12/2019] [Accepted: 01/18/2019] [Indexed: 01/16/2023]
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Fief CA, Hoang KG, Phipps SD, Wallace JL, Deweese JE. Examining the Impact of Antimicrobial Fluoroquinolones on Human DNA Topoisomerase IIα and IIβ. ACS OMEGA 2019; 4:4049-4055. [PMID: 31459613 PMCID: PMC6648947 DOI: 10.1021/acsomega.8b03428] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/11/2019] [Indexed: 05/29/2023]
Abstract
Fluoroquinolones are a class of widely prescribed antibiotics with a broad range of activity against Gram-positive, Gram-negative, and some atypical microbes. Unfortunately, these drugs are associated with significant adverse events including neuropathy, tendinopathy, cardiac rhythm abnormalities, and mental health side effects. The mechanism by which fluoroquinolones cause many of these toxicities is unknown. The antibacterial mechanism of action involves disruption of the catalytic mechanism of type-II topoisomerases in bacteria, namely topoisomerase IV and DNA gyrase. Fluoroquinolones inhibit the ability of the enzymes to ligate cleaved DNA and result in single- and double-stranded DNA breaks. Thus, there is an interest in investigating whether human topoisomerase II is involved in mediating the adverse events associated with quinolones. Previous studies demonstrate some response of human topoisomerase IIα and IIβ to high levels of ciprofloxacin. However, it is not clear whether the concentration of ciprofloxacin utilized in those studies corresponds to concentrations that would be routinely achievable in patients. Therefore, this study set out to examine three clinically relevant fluoroquinolones along with two older agents to determine whether these compounds display activity against topoisomerase IIα and IIβ at drug concentrations that more closely approximate typical patient plasma values. On the basis of our evidence, none of the quinolones studied were able to poison DNA cleavage by either human enzyme. Ciprofloxacin, desethylene-ciprofloxacin, and the recently removed from market gemifloxacin were able to inhibit topoisomerase II-mediated DNA relaxation at concentrations of 200-300 μM. On the basis of these data, we propose that human topoisomerase II is not likely to be the main cause of these adverse events and that additional targets need to be identified to clarify the mechanisms underlying quinolone toxicities.
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Affiliation(s)
- Cole A. Fief
- Department
of Pharmaceutical Sciences and Department of Pharmacy Practice, Lipscomb University College of Pharmacy and Health
Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Kristine G. Hoang
- Department
of Pharmaceutical Sciences and Department of Pharmacy Practice, Lipscomb University College of Pharmacy and Health
Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Stephen D. Phipps
- Department
of Pharmaceutical Sciences and Department of Pharmacy Practice, Lipscomb University College of Pharmacy and Health
Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
| | - Jessica L. Wallace
- Department
of Pharmaceutical Sciences and Department of Pharmacy Practice, Lipscomb University College of Pharmacy and Health
Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
- Veterans
Affairs Tennessee Valley Healthcare System, 1310 24th, Avenue South, Nashville, Tennessee 37232, United States
| | - Joseph E. Deweese
- Department
of Pharmaceutical Sciences and Department of Pharmacy Practice, Lipscomb University College of Pharmacy and Health
Sciences, One University Park Drive, Nashville, Tennessee 37204-3951, United States
- Department
of Biochemistry, Vanderbilt University School
of Medicine, 2215 Garland
Avenue, Nashville, Tennessee 37232-0146, United States
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Sangpheak K, Mueller M, Darai N, Wolschann P, Suwattanasophon C, Ruga R, Chavasiri W, Seetaha S, Choowongkomon K, Kungwan N, Rungnim C, Rungrotmongkol T. Computational screening of chalcones acting against topoisomerase IIα and their cytotoxicity towards cancer cell lines. J Enzyme Inhib Med Chem 2018; 34:134-143. [PMID: 30394113 PMCID: PMC6225485 DOI: 10.1080/14756366.2018.1507029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Targeted cancer therapy has become one of the high potential cancer treatments. Human topoisomerase II (hTopoII), which catalyzes the cleavage and rejoining of double-stranded DNA, is an important molecular target for the development of novel cancer therapeutics. In order to diversify the pharmacological activity of chalcones and to extend the scaffold of topoisomerase inhibitors, a series of chalcones was screened against hTopoIIα by computational techniques, and subsequently tested for their in vitro cytotoxicity. From the experimental IC50 values, chalcone 3d showed a high cytotoxicity with IC50 values of 10.8, 3.2 and 21.1 µM against the HT-1376, HeLa and MCF-7 cancer-derived cell lines, respectively, and also exhibited an inhibitory activity against hTopoIIα-ATPase that was better than the known inhibitor, salvicine. The observed ligand-protein interactions from a molecular dynamics study affirmed that 3d strongly interacts with the ATP-binding pocket residues. Altogether, the newly synthesised chalcone 3d has a high potential to serve as a lead compound for topoisomerase inhibitors.
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Affiliation(s)
- Kanyani Sangpheak
- a Faculty of Science, Program in Biotechnology , Chulalongkorn University , Bangkok , Thailand
| | - Monika Mueller
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria
| | - Nitchakan Darai
- a Faculty of Science, Program in Biotechnology , Chulalongkorn University , Bangkok , Thailand
| | - Peter Wolschann
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria.,c Institute of Theoretical Chemistry , University of Vienna , Vienna , Austria
| | - Chonticha Suwattanasophon
- b Department of Pharmaceutical Technology and Biopharmaceutics , University of Vienna , Vienna , Austria
| | - Ritbey Ruga
- d Faculty of Science, Center of Excellence in Natural Products Chemistry, Department of Chemistry , Chulalongkorn University , Bangkok , Thailand
| | - Warinthon Chavasiri
- d Faculty of Science, Center of Excellence in Natural Products Chemistry, Department of Chemistry , Chulalongkorn University , Bangkok , Thailand
| | - Supaporn Seetaha
- e Faculty of Science, Department of Biochemistry , Kasetsart University , Bangkok , Thailand
| | - Kiattawee Choowongkomon
- e Faculty of Science, Department of Biochemistry , Kasetsart University , Bangkok , Thailand
| | - Nawee Kungwan
- f Faculty of Science, Department of Chemistry , Chiang Mai University , Chiang Mai , Thailand.,g Center of Excellence in Materials Science and Technology , Chiang Mai University , Chiang Mai , Thailand
| | - Chompoonut Rungnim
- h Nanoscale Simulation Laboratory, National Nanotechnology Center , National Science and Technology Development Agency , Pathum Thani , Thailand
| | - Thanyada Rungrotmongkol
- i Faculty of Science, Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry , Chulalongkorn University , Bangkok , Thailand.,j Faculty of Science, Ph.D. Program in Bioinformatics and Computational Biology , Chulalongkorn University , Bangkok , Thailand
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Hevener K, Verstak TA, Lutat KE, Riggsbee DL, Mooney JW. Recent developments in topoisomerase-targeted cancer chemotherapy. Acta Pharm Sin B 2018; 8:844-861. [PMID: 30505655 PMCID: PMC6251812 DOI: 10.1016/j.apsb.2018.07.008] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/17/2022] Open
Abstract
The DNA topoisomerase enzymes are essential to cell function and are found ubiquitously in all domains of life. The various topoisomerase enzymes perform a wide range of functions related to the maintenance of DNA topology during DNA replication, and transcription are the targets of a wide range of antimicrobial and cancer chemotherapeutic agents. Natural product-derived agents, such as the camptothecin, anthracycline, and podophyllotoxin drugs, have seen broad use in the treatment of many types of cancer. Selective targeting of the topoisomerase enzymes for cancer treatment continues to be a highly active area of basic and clinical research. The focus of this review will be to summarize the current state of the art with respect to clinically used topoisomerase inhibitors for targeted cancer treatment and to discuss the pharmacology and chemistry of promising new topoisomerase inhibitors in clinical and pre-clinical development.
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Affiliation(s)
- KirkE. Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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