1
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Herlah B, Pavlin M, Perdih A. Molecular choreography: Unveiling the dynamic landscape of type IIA DNA topoisomerases before T-segment passage through all-atom simulations. Int J Biol Macromol 2024; 269:131991. [PMID: 38714283 DOI: 10.1016/j.ijbiomac.2024.131991] [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: 01/09/2024] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024]
Abstract
Type IIA DNA topoisomerases are molecular nanomachines responsible for controlling topological states of DNA molecules. Here, we explore the dynamic landscape of yeast topoisomerase IIA during key stages of its catalytic cycle, focusing in particular on the events preceding the passage of the T-segment. To this end, we generated six configurations of fully catalytic yeast topo IIA, strategically inserted a T-segment into the N-gate in relevant configurations, and performed all-atom simulations. The essential motion of topo IIA protein dimer was characterized by rotational gyrating-like movement together with sliding motion within the DNA-gate. Both appear to be inherent properties of the enzyme and an inbuilt feature that allows passage of the T-segment through the cleaved G-segment. Coupled dynamics of the N-gate and DNA-gate residues may be particularly important for controlled and smooth passage of the T-segment and consequently the prevention of DNA double-strand breaks. QTK loop residue Lys367, which interacts with ATP and ADP molecules, is involved in regulating the size and stability of the N-gate. The unveiled features of the simulated configurations provide insights into the catalytic cycle of type IIA topoisomerases and elucidate the molecular choreography governing their ability to modulate the topological states of DNA topology.
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Affiliation(s)
- Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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2
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Cong J, Xin Y, Kang H, Yang Y, Wang C, Zhao D, Li X, Rao Z, Chen Y. Structural insights into the DNA topoisomerase II of the African swine fever virus. Nat Commun 2024; 15:4607. [PMID: 38816407 PMCID: PMC11139879 DOI: 10.1038/s41467-024-49047-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus.
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Affiliation(s)
- Jingyuan Cong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuhui Xin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huiling Kang
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Yunge Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenlong Wang
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Dongming Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China.
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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3
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Endsley CE, Moore KA, Townsley TD, Durston KK, Deweese JE. Bioinformatic Analysis of Topoisomerase IIα Reveals Interdomain Interdependencies and Critical C-Terminal Domain Residues. Int J Mol Sci 2024; 25:5674. [PMID: 38891861 PMCID: PMC11172036 DOI: 10.3390/ijms25115674] [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: 03/23/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
DNA Topoisomerase IIα (Top2A) is a nuclear enzyme that is a cancer drug target, and there is interest in identifying novel sites on the enzyme to inhibit cancer cells more selectively and to reduce off-target toxicity. The C-terminal domain (CTD) is one potential target, but it is an intrinsically disordered domain, which prevents structural analysis. Therefore, we set out to analyze the sequence of Top2A from 105 species using bioinformatic analysis, including the PSICalc algorithm, Shannon entropy analysis, and other approaches. Our results demonstrate that large (10th-order) interdependent clusters are found including non-proximal positions across the major domains of Top2A. Further, CTD-specific clusters of the third, fourth, and fifth order, including positions that had been previously analyzed via mutation and biochemical assays, were identified. Some of these clusters coincided with positions that, when mutated, either increased or decreased relaxation activity. Finally, sites of low Shannon entropy (i.e., low variation in amino acids at a given site) were identified and mapped as key positions in the CTD. Included in the low-entropy sites are phosphorylation sites and charged positions. Together, these results help to build a clearer picture of the critical positions in the CTD and provide potential sites/regions for further analysis.
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Affiliation(s)
- Clark E. Endsley
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | - Kori A. Moore
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
| | | | - Kirk K. Durston
- Department of Research and Publications, Digital Strategies, Langley, BC V2Y 1N5, Canada
| | - Joseph E. Deweese
- Biological, Physical, and Human Sciences Department, Freed-Hardeman University, Henderson, TN 38340, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
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4
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Oviatt A, Gibson EG, Huang J, Mattern K, Neuman KC, Chan PF, Osheroff N. Interactions between Gepotidacin and Escherichia coli Gyrase and Topoisomerase IV: Genetic and Biochemical Evidence for Well-Balanced Dual-Targeting. ACS Infect Dis 2024; 10:1137-1151. [PMID: 38606465 PMCID: PMC11015057 DOI: 10.1021/acsinfecdis.3c00346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance is a global threat to human health. Therefore, efforts have been made to develop new antibacterial agents that address this critical medical issue. Gepotidacin is a novel, bactericidal, first-in-class triazaacenaphthylene antibacterial in clinical development. Recently, phase III clinical trials for gepotidacin treatment of uncomplicated urinary tract infections caused by uropathogens, including Escherichia coli, were stopped for demonstrated efficacy. Because of the clinical promise of gepotidacin, it is important to understand how the compound interacts with its cellular targets, gyrase and topoisomerase IV, from E. coli. Consequently, we determined how gyrase and topoisomerase IV mutations in amino acid residues that are involved in gepotidacin interactions affect the susceptibility of E. coli cells to the compound and characterized the effects of gepotidacin on the activities of purified wild-type and mutant gyrase and topoisomerase IV. Gepotidacin displayed well-balanced dual-targeting of gyrase and topoisomerase IV in E. coli cells, which was reflected in a similar inhibition of the catalytic activities of these enzymes by the compound. Gepotidacin induced gyrase/topoisomerase IV-mediated single-stranded, but not double-stranded, DNA breaks. Mutations in GyrA and ParC amino acid residues that interact with gepotidacin altered the activity of the compound against the enzymes and, when present in both gyrase and topoisomerase IV, reduced the antibacterial activity of gepotidacin against this mutant strain. Our studies provide insights regarding the well-balanced dual-targeting of gyrase and topoisomerase IV by gepotidacin in E. coli.
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Affiliation(s)
- Alexandria
A. Oviatt
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Elizabeth G. Gibson
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Department
of Pharmacology, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Jianzhong Huang
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Karen Mattern
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Keir C. Neuman
- Laboratory
of Single Molecule Biophysics, National
Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20982, United States
| | - Pan F. Chan
- Infectious
Diseases Research Unit, GlaxoSmithKline, Collegeville, Pennsylvania 19426, 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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5
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Collins J, Osheroff N. Gyrase and Topoisomerase IV: Recycling Old Targets for New Antibacterials to Combat Fluoroquinolone Resistance. ACS Infect Dis 2024; 10:1097-1115. [PMID: 38564341 PMCID: PMC11019561 DOI: 10.1021/acsinfecdis.4c00128] [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: 02/16/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Beyond their requisite functions in many critical DNA processes, the bacterial type II topoisomerases, gyrase and topoisomerase IV, are the targets of fluoroquinolone antibacterials. These drugs act by stabilizing gyrase/topoisomerase IV-generated DNA strand breaks and by robbing the cell of the catalytic activities of these essential enzymes. Since their clinical approval in the mid-1980s, fluoroquinolones have been used to treat a broad spectrum of infectious diseases and are listed among the five "highest priority" critically important antimicrobial classes by the World Health Organization. Unfortunately, the widespread use of fluoroquinolones has been accompanied by a rise in target-mediated resistance caused by specific mutations in gyrase and topoisomerase IV, which has curtailed the medical efficacy of this drug class. As a result, efforts are underway to identify novel antibacterials that target the bacterial type II topoisomerases. Several new classes of gyrase/topoisomerase IV-targeted antibacterials have emerged, including novel bacterial topoisomerase inhibitors, Mycobacterium tuberculosis gyrase inhibitors, triazaacenaphthylenes, spiropyrimidinetriones, and thiophenes. Phase III clinical trials that utilized two members of these classes, gepotidacin (triazaacenaphthylene) and zoliflodacin (spiropyrimidinetrione), have been completed with positive outcomes, underscoring the potential of these compounds to become the first new classes of antibacterials introduced into the clinic in decades. Because gyrase and topoisomerase IV are validated targets for established and emerging antibacterials, this review will describe the catalytic mechanism and cellular activities of the bacterial type II topoisomerases, their interactions with fluoroquinolones, the mechanism of target-mediated fluoroquinolone resistance, and the actions of novel antibacterials against wild-type and fluoroquinolone-resistant gyrase and topoisomerase IV.
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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
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6
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Kour P, Saha P, Sharma DK, Singh K. DNA topoisomerases as a drug target in Leishmaniasis: Structural and mechanistic insights. Int J Biol Macromol 2024; 256:128401. [PMID: 38007027 DOI: 10.1016/j.ijbiomac.2023.128401] [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: 06/10/2023] [Revised: 11/09/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
Leishmaniasis, caused by a protozoan parasite, is among humanity's costliest banes, owing to the high mortality and morbidity ratio in poverty-stricken areas. To date, no vaccine is available for the complete cure of the disease. Current chemotherapy is expensive, has undesirable side effects, and faces drug resistance limitations and toxicity concerns. The substantial differences in homology between leishmanial DNA topoisomerase IB compared with the human counterparts provided a new lead in the study of the structural determinants that can be targeted. Several research groups explored this molecular target, trying to fill the therapeutic gap, and came forward with various anti-leishmanial scaffolds. This article is a comprehensive review of knowledge about topoisomerases as an anti-leishmanial drug target and their inhibitors collected over the years. In addition to information on molecular targets and reported scaffolds, the review details the structure-activity relationship of described compounds with leishmanial Topoisomerase IB. Moreover, the work also includes information about the structure of the inhibitors, showing common interacting residues with leishmanial topoisomerases that drive their mode of action towards them. Finally, in search of topoisomerase inhibitors at the stage of clinical trials, we have listed all the drugs that have been in clinical trials against leishmaniasis.
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Affiliation(s)
- Parampreet Kour
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Pallavi Saha
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology Banaras Hindu University, Varanasi 221005, India
| | - Deepak K Sharma
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology Banaras Hindu University, Varanasi 221005, India
| | - Kuljit Singh
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. CRISPR J 2023; 6:527-542. [PMID: 38108519 PMCID: PMC10753984 DOI: 10.1089/crispr.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 11/10/2023] [Indexed: 12/19/2023] Open
Abstract
To protect against mobile genetic elements (MGEs), some bacteria and archaea have clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) adaptive immune systems. CRISPR RNAs (crRNAs) bound to Cas nucleases hybridize to MGEs based on sequence complementarity to guide the nucleases to cleave the MGEs. This programmable DNA cleavage has been harnessed for gene editing. Safety concerns include off-target and guide RNA (gRNA)-free DNA cleavages, both of which are observed in the Cas nuclease commonly used for gene editing, Streptococcus pyogenes Cas9 (SpyCas9). We developed a SpyCas9 variant (SpyCas9H982A) devoid of gRNA-free DNA cleavage activity that is more selective for on-target cleavage. The H982A substitution in the metal-dependent RuvC active site reduces Mn2+-dependent gRNA-free DNA cleavage by ∼167-fold. Mechanistic molecular dynamics analysis shows that Mn2+, but not Mg2+, produces a gRNA-free DNA cleavage competent state that is disrupted by the H982A substitution. Our study demonstrates the feasibility of modulating cation:protein interactions to engineer safer gene editing tools.
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Affiliation(s)
- Sydney N. Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Isabelle Schuster
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Yadin G. Joseph
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, The University of Oklahoma, Norman, Oklahoma, USA
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8
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Pavlin M, Herlah B, Valjavec K, Perdih A. Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations: Implications for understanding its catalytic cycle. Comput Struct Biotechnol J 2023; 21:3746-3759. [PMID: 37602233 PMCID: PMC10436251 DOI: 10.1016/j.csbj.2023.07.019] [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: 04/23/2023] [Revised: 07/01/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.
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Affiliation(s)
- Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Katja Valjavec
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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9
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Jian JY, Osheroff N. Telling Your Right Hand from Your Left: The Effects of DNA Supercoil Handedness on the Actions of Type II Topoisomerases. Int J Mol Sci 2023; 24:11199. [PMID: 37446377 PMCID: PMC10342825 DOI: 10.3390/ijms241311199] [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: 06/16/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Type II topoisomerases are essential enzymes that modulate the topological state of DNA supercoiling in all living organisms. These enzymes alter DNA topology by performing double-stranded passage reactions on over- or underwound DNA substrates. This strand passage reaction generates a transient covalent enzyme-cleaved DNA structure known as the cleavage complex. Al-though the cleavage complex is a requisite catalytic intermediate, it is also intrinsically dangerous to genomic stability in biological systems. The potential threat of type II topoisomerase function can also vary based on the nature of the supercoiled DNA substrate. During essential processes such as DNA replication and transcription, cleavage complex formation can be inherently more dangerous on overwound versus underwound DNA substrates. As such, it is important to understand the profound effects that DNA topology can have on the cellular functions of type II topoisomerases. This review will provide a broad assessment of how human and bacterial type II topoisomerases recognize and act on their substrates of various topological states.
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Affiliation(s)
- Jeffrey Y. Jian
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, 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
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10
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Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [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: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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11
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Lenin B, Ramasubramanyan S, Vetrivel U, Chitipothu S. Virtual screening and multilevel precision-based prioritisation of natural inhibitors targeting the ATPase domain of human DNA topoisomerase II alpha. J Biomol Struct Dyn 2023; 41:15177-15195. [PMID: 36898858 DOI: 10.1080/07391102.2023.2187234] [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: 11/15/2022] [Accepted: 02/25/2023] [Indexed: 03/12/2023]
Abstract
Human DNA topoisomerase II alpha (hTopIIα) is a classic chemotherapeutic drug target. The existing hTopIIα poisons cause numerous side effects such as the development of cardiotoxicity, secondary malignancies, and multidrug resistance. The use of catalytic inhibitors targeting the ATP-binding cavity of the enzyme is considered a safer alternative due to the less deleterious mechanism of action. Hence, in this study, we carried out high throughput structure-based virtual screening of the NPASS natural product database against the ATPase domain of hTopIIα and identified the five best ligand hits. This was followed by comprehensive validation through molecular dynamics simulations, binding free energy calculation and ADMET analysis. On stringent multilevel prioritization, we identified promising natural product catalytic inhibitors that showed high binding affinity and stability within the ligand-binding cavity and may serve as ideal hits for anticancer drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Barathi Lenin
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Sharada Ramasubramanyan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, Karnataka, India
| | - Srujana Chitipothu
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
- Central Research Instrumentation Facility, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
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12
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Kaur R, Aboelnga MM, Nikkel DJ, Wetmore SD. The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme. Phys Chem Chem Phys 2022; 24:29130-29140. [PMID: 36444615 DOI: 10.1039/d2cp04338f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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13
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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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14
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Prototype Foamy Virus Integrase Displays Unique Biochemical Activities among Retroviral Integrases. Biomolecules 2021; 11:biom11121910. [PMID: 34944553 PMCID: PMC8699820 DOI: 10.3390/biom11121910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/01/2022] Open
Abstract
Integrases of different retroviruses assemble as functional complexes with varying multimers of the protein. Retroviral integrases require a divalent metal cation to perform one-step transesterification catalysis. Tetrameric prototype foamy virus (PFV) intasomes assembled from purified integrase and viral DNA oligonucleotides were characterized for their activity in the presence of different cations. While most retroviral integrases are inactive in calcium, PFV intasomes appear to be uniquely capable of catalysis in calcium. The PFV intasomes also contrast with other retroviral integrases by displaying an inverse correlation of activity with increasing manganese beginning at relatively low concentrations. The intasomes were found to be significantly more active in the presence of chloride co-ions compared to acetate. While HIV-1 integrase appears to commit to a target DNA within 20 s, PFV intasomes do not commit to target DNA during their reaction lifetime. Together, these data highlight the unique biochemical activities of PFV integrase compared to other retroviral integrases.
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15
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Topoisomerase poisoning by the flavonoid nevadensin triggers DNA damage and apoptosis in human colon carcinoma HT29 cells. Arch Toxicol 2021; 95:3787-3802. [PMID: 34635930 PMCID: PMC8536574 DOI: 10.1007/s00204-021-03162-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]
Abstract
Nevadensin, an abundant polyphenol of basil, is reported to reduce alkenylbenzene DNA adduct formation. Furthermore, it has a wide spectrum of further pharmacological properties. The presented study focuses the impact of nevadensin on topoisomerases (TOPO) in vitro. Considering the DNA-intercalating properties of flavonoids, first, minor groove binding properties (IC50 = 31.63 µM), as well as DNA intercalation (IC50 = 296.91 µM) of nevadensin, was found. To determine potential in vitro effects on TOPO I and TOPO IIα, the relaxation and decatenation assay was performed in a concentration range of 1–500 µM nevadensin. A partial inhibition was detected for TOPO I at concentrations ≥ 100 µM, whereas TOPO IIα activity is only inhibited at concentrations ≥ 250 µM. To clarify the mode of action, the isolating in vivo complex of enzyme assay was carried out using human colon carcinoma HT29 cells. After 1 h of incubation, the amount of TOPO I linked to DNA was significantly increased by nevadensin (500 µM), why nevadensin was characterized as TOPO I poison. However, no effects on TOPO IIα were detected in the cellular test system. As a subsequent cellular response to TOPO I poisoning, a highly significant increase of DNA damage after 2 h and a decrease of cell viability after 48 h at the same concentration range were found. Furthermore, after 24 h of incubation a G2/M arrest was observed at concentrations ≥ 100 µM by flow cytometry. The analysis of cell death revealed that nevadensin induces the intrinsic apoptotic pathway via activation of caspase-9 and caspase-3. The results suggest that cell cycle disruption and apoptotic events play key roles in the cellular response to TOPO I poisoning caused by nevadensin in HT29 cells.
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16
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Pachanon R, Koide K, Kongsoi S, Ajima N, Kapalamula TF, Nakajima C, Suthienkul O, Suzuki Y. Effectiveness of Fluoroquinolones with Difluoropyridine Derivatives as R1 Groups on the Salmonella DNA Gyrase in the Presence and Absence of Plasmid-Encoded Quinolone Resistance Protein QnrB19. Microb Drug Resist 2021; 27:1412-1419. [PMID: 33835868 DOI: 10.1089/mdr.2020.0455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: WQ-3810 has strong inhibitory activity against Salmonella and other fluoroquinolone-resistant pathogens. The unique potentiality of this is attributed to 6-amino-3,5-difluoropyridine-2-yl at R1 group. The aim of this study was to examine WQ-3810 and its derivatives WQ-3334 and WQ-4065 as the new drug candidate for wild-type Salmonella and that carrying QnrB19. Materials and Methods: The half maximal inhibitory concentrations (IC50s) of WQ-3810, WQ-3334 (Br atom in place of methyl group at R8), and WQ-4065 (6-ethylamino-3,5-difluoropyridine-2-yl in place of 6-amino-3,5-difluoropyridine-2-yl group at R1) in the presence or absence of QnrB19 were assessed by in vitro DNA supercoiling assay utilizing recombinant DNA gyrase and QnrB19. Results: IC50s of WQ-3810, WQ-3334, and WQ-4065 against Salmonella DNA gyrase were 0.031 ± 0.003, 0.068 ± 0.016, and 0.72 ± 0.39 μg/mL, respectively, while QnrB19 increased IC50s of WQ-3810, WQ-3334, and WQ-4065 to 0.44 ± 0.05, 0.92 ± 0.34, and 9.16 ± 2.21 μg/mL, respectively. Conclusion: WQ-3810 and WQ-3334 showed stronger inhibitory activity against Salmonella Typhimurium DNA gyrases than WQ-4065 even in the presence of QnrB19. The results suggest that 6-amino-3,5-difluoropyridine-2-yl group at R1 is playing an important role and WQ-3810 and WQ-3334 to be good candidates for Salmonella carrying QnrB19.
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Affiliation(s)
- Ruttana Pachanon
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Koide
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Siriporn Kongsoi
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Nami Ajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Station for Zoonosis Control, The Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Orasa Suthienkul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Salaya, Thailand
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Station for Zoonosis Control, The Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
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17
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Pachanon R, Koide K, Kongsoi S, Nakajima C, Kapalamula TF, Suthienkul O, Suzuki Y. Interaction of the plasmid-encoded quinolone resistance protein QnrB19 with Salmonella Typhimurium DNA gyrase. J Infect Chemother 2020; 26:1139-1145. [PMID: 32669211 DOI: 10.1016/j.jiac.2020.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Plasmid-encoded quinolone resistance protein Qnr is an important factor in bacterial resistance to quinolones. Qnr interacts with DNA gyrase and reduces susceptibility to quinolones. The gene qnr likely spreads rapidly among Enterobacteriaceae via horizontal gene transfer. Though the vast amounts of epidemiological data are available, molecular details of the contribution of QnrB19, the predominant Qnr in Salmonella spp., to the acquisition of quinolone resistance has not yet been understood well. OBJECTIVE We aimed to examine the role of QnrB19 in quinolone resistance acquisition using recombinant Salmonella Typhimurium DNA gyrases and QnrB19. MATERIALS AND METHODS Recombinant QnrB19 was expressed in E. coli and purified by Ni-NTA agarose column chromatography. DNA supercoiling activities of recombinant Salmonella Typhimurium DNA gyrase were assessed with or without QnrB19 under the existence of three quinolones to measure IC50s, the concentration of each quinolone required for 50% inhibition in vitro. RESULTS The IC50s of norfloxacin, ciprofloxacin and nalidixic acid against DNA gyrases were measured to be 0.30, 0.16 and 17.7 μg/mL, respectively. The addition of QnrB19 increased the IC50s of norfloxacin and ciprofloxacin to be 0.81 and 0.48 μg/mL, respectively, where no effect of QnrB19 was observed on the IC50 of nalidixic acid. CONCLUSION QnrB19 was shown for the first time in vitro to have ability to grant non-classical quinolone resistance to S. Typhimurium DNA gyrase. Structural insight on quinolones in this study may contribute to investigate drugs useful for preventing the spread of plasmid carrying PMQR along with other factors associating with antimicrobial resistance in S. Typhimurium and other bacteria.
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Affiliation(s)
- Ruttana Pachanon
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Japan
| | - Kentaro Koide
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Japan
| | | | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Japan; Global Station for Zoonosis Control, Hokkaido University, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Japan
| | - Orasa Suthienkul
- Center of Education and Research in EcoHealth and OneHealth, Faculty of Public Health, Thammasat University, Thailand; Center of Excellence in Global Health, Faculty of Public Health, Thammasat University, Thailand
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Japan; Global Station for Zoonosis Control, Hokkaido University, Japan.
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18
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Discovery of new ATP-competitive inhibitors of human DNA topoisomerase IIα through screening of bacterial topoisomerase inhibitors. Bioorg Chem 2020; 102:104049. [PMID: 32688116 DOI: 10.1016/j.bioorg.2020.104049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Human DNA topoisomerase II is one of the major targets in anticancer therapy, however ATP-competitive inhibitors of this target have not yet reached their full potential. ATPase domain of human DNA topoisomerase II belongs to the GHKL ATPase superfamily and shares a very high 3D structural similarity with other superfamily members, including bacterial topoisomerases. In this work we report the discovery of a new chemotype of ATP-competitive inhibitors of human DNA topoisomerase IIα that were discovered through screening of in-house library of ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV. Systematic screening of this library provided us with 20 hit compounds. 1,2,4-Substituted N-phenylpyrrolamides were selected for a further exploration which resulted in 13 new analogues, including 52 with potent activity in relaxation assay (IC50 = 3.2 µM) and ATPase assay (IC50 = 0.43 µM). Cytotoxic activity of all hits was determined in MCF-7 cancer cell line and the most potent compounds, 16 and 20, showed an IC50 value of 8.7 and 8.2 µM, respectively.
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19
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Park S, Hwang SY, Shin J, Jo H, Na Y, Kwon Y. A chromenone analog as an ATP-competitive, DNA non-intercalative topoisomerase II catalytic inhibitor with preferences toward the alpha isoform. Chem Commun (Camb) 2019; 55:12857-12860. [PMID: 31598611 DOI: 10.1039/c9cc05524j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
5-Hydroxy-2-phenyl-7-(thiiran-2-ylmethoxy)-4H-chromen-4-one (compound 52) was found as a DNA non-intercalative topo II specific catalytic inhibitor by targeting its ATP-binding domain. Showing changes in interaction with Mg2+, it exhibited highly selective properties against the α-isoform with less toxicity, unlike other topo II poisons, such as etoposide.
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Affiliation(s)
- Seojeong Park
- College of Pharmacy & Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea.
| | - Soo-Yeon Hwang
- College of Pharmacy & Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea.
| | - Jaeho Shin
- College of Pharmacy, CHA University, Pocheon, 11160, Korea.
| | - Hyunji Jo
- College of Pharmacy & Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea.
| | - Younghwa Na
- College of Pharmacy, CHA University, Pocheon, 11160, Korea.
| | - Youngjoo Kwon
- College of Pharmacy & Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Korea.
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20
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Kuriappan JA, Osheroff N, De Vivo M. Smoothed Potential MD Simulations for Dissociation Kinetics of Etoposide To Unravel Isoform Specificity in Targeting Human Topoisomerase II. J Chem Inf Model 2019; 59:4007-4017. [PMID: 31449404 PMCID: PMC6800198 DOI: 10.1021/acs.jcim.9b00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Human
type II topoisomerases (TopoII) are essential for controlling
DNA topology within the cell. For this reason, there are a number
of TopoII-targeted anticancer drugs that act by inducing DNA cleavage
mediated by both TopoII isoforms (TopoIIα and TopoIIβ)
in cells. However, recent studies suggest that specific poisoning
of TopoIIα may be a safer strategy for treating cancer. This
is because poisoning of TopoIIβ appears to be linked to the
generation of secondary leukemia in patients. We recently reported
that enzyme-mediated DNA cleavage complexes (in which TopoII is covalently
linked to the cleaved DNA during catalysis) formed in the presence
of the anticancer drug etoposide persisted approximately 3-fold longer
with TopoIIα than TopoIIβ. Notably, enhanced drug-target
residence time may reduce the adverse effects of specific TopoIIα
poisons. However, it is still not clear how to design drugs that are
specific for the α isoform. In this study, we report the results
of classical molecular dynamics (MD) simulations to comparatively
analyze the molecular interactions formed within the TopoII/DNA/etoposide
complex with both isoforms. We also used smoothed potential MD to
estimate etoposide dissociation kinetics from the two isoform complexes.
These extensive classical and enhanced sampling simulations revealed
stabilizing interactions of etoposide with two serine residues (Ser763
and Ser800) in TopoIIα. These interactions are missing in TopoIIβ,
where both amino acids are alanine residues. This may explain the
greater persistence of etoposide-stabilized cleavage complexes formed
with Topo TopoIIα. These findings could be useful for the rational
design of specific TopoIIα poisons.
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Affiliation(s)
- Jissy A Kuriappan
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genova , 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 Genova , Italy
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21
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Cao N, Tan K, Annamalai T, Joachimiak A, Tse-Dinh YC. Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site. Nucleic Acids Res 2019; 46:7296-7308. [PMID: 29905859 PMCID: PMC6101483 DOI: 10.1093/nar/gky492] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/18/2022] Open
Abstract
We have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.
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Affiliation(s)
- Nan Cao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Kemin Tan
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA.,Biomolecular Sciences Institute, Florida International University, 11200 SW 8 St, Miami, FL 33199, USA
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22
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DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion. J Mol Biol 2019; 431:3427-3449. [PMID: 31301408 PMCID: PMC6723622 DOI: 10.1016/j.jmb.2019.07.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022]
Abstract
Type II topoisomerases regulate DNA topology by making a double-stranded break in one DNA duplex, transporting another DNA segment through this break and then resealing it. Bacterial type IIA topoisomerase inhibitors, such as fluoroquinolones and novel bacterial topoisomerase inhibitors, can trap DNA cleavage complexes with double- or single-stranded cleaved DNA. To study the mode of action of such compounds, 21 crystal structures of a “gyraseCORE” fusion truncate of Staphyloccocus aureus DNA gyrase complexed with DNA and diverse inhibitors have been published, as well as 4 structures lacking inhibitors. These structures have the DNA in various cleavage states and appear to track trajectories along the catalytic paths of the DNA cleavage/religation steps. The various conformations sampled by these multiple “gyraseCORE” structures show rigid body movements of the catalytic GyrA WHD and GyrB TOPRIM domains across the dimer interface. Conformational changes common to all compound-bound structures suggest common mechanisms for DNA cleavage-stabilizing compounds. The structures suggest that S. aureus gyrase uses a single moving-metal ion for cleavage and that the central four base pairs need to be stretched between the two catalytic sites, in order for a scissile phosphate to attract a metal ion to the A-site to catalyze cleavage, after which it is “stored” in another coordination configuration (B-site) in the vicinity. We present a simplified model for the catalytic cycle in which capture of the transported DNA segment causes conformational changes in the ATPase domain that push the DNA gate open, resulting in stretching and cleaving the gate-DNA in two steps. Type II DNA topoisomerases, such as DNA gyrase, control the topological state of DNA in all cells. As these enzymes bind, cleave and re-ligate DNA, multiple binding pockets for small compounds appear. We discuss how crystal structures of gyrase, DNA and different compounds may be trapping different stages in the catalytic cycle of the enzyme. We propose a model for DNA strand cleavage involving a moving metal ion.
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23
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Jang Y, Son H, Lee SW, Hwang W, Jung SR, Byl JAW, Osheroff N, Lee S. Selection of DNA Cleavage Sites by Topoisomerase II Results from Enzyme-Induced Flexibility of DNA. Cell Chem Biol 2019; 26:502-511.e3. [PMID: 30713098 DOI: 10.1016/j.chembiol.2018.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/04/2018] [Accepted: 12/04/2018] [Indexed: 12/26/2022]
Abstract
Topoisomerase II cleaves DNA at preferred sequences with different efficiencies; however, the mechanism of cleavage site selection is not known. Here we used single-molecule fluorescence assays that monitor several critical steps of DNA-topoisomerase II interactions, including binding/dissociation, bending/straightening, and cleavage/religation, and reveal that the cleavage site is selected mainly during the bending step. Furthermore, despite the sensitivity of the bending rate to the DNA sequence, it is not an intrinsic property of the DNA itself. Rather, it is determined by protein-DNA interactions.
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Affiliation(s)
- Yunsu Jang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Heyjin Son
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Sang-Wook Lee
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Wonseok Hwang
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Seung-Ryoung Jung
- Department of Physics and Astronomy, National Center for Creative Research Initiatives, Seoul National University, Seoul 08826, South Korea
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; VA Tennessee Valley Healthcare System, Nashville, TN 37212, USA.
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea.
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24
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Jung SR, Lee SW, Hohng S. Real-Time Monitoring of the Binding/Dissociation and Redox States of a Single Transition Metal Ions. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Seung-Ryoung Jung
- Department of Physics and Astronomy; Seoul National University; Seoul Republic of Korea
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
| | - Sang-Wook Lee
- Department of Physics and Astronomy; Seoul National University; Seoul Republic of Korea
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
| | - Sungchul Hohng
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
- Institute of Applied Physics, Seoul National University; Seoul Republic of Korea
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25
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Infante Lara L, Fenner S, Ratcliffe S, Isidro-Llobet A, Hann M, Bax B, Osheroff N. Coupling the core of the anticancer drug etoposide to an oligonucleotide induces topoisomerase II-mediated cleavage at specific DNA sequences. Nucleic Acids Res 2018; 46:2218-2233. [PMID: 29447373 PMCID: PMC5861436 DOI: 10.1093/nar/gky072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/18/2018] [Accepted: 02/06/2018] [Indexed: 12/13/2022] Open
Abstract
Etoposide and other topoisomerase II-targeted drugs are important anticancer therapeutics. Unfortunately, the safe usage of these agents is limited by their indiscriminate induction of topoisomerase II-mediated DNA cleavage throughout the genome and by a lack of specificity toward cancer cells. Therefore, as a first step toward constraining the distribution of etoposide-induced DNA cleavage sites and developing sequence-specific topoisomerase II-targeted anticancer agents, we covalently coupled the core of etoposide to oligonucleotides centered on a topoisomerase II cleavage site in the PML gene. The initial sequence used for this 'oligonucleotide-linked topoisomerase inhibitor' (OTI) was identified as part of the translocation breakpoint of a patient with acute promyelocytic leukemia (APL). Subsequent OTI sequences were derived from the observed APL breakpoint between PML and RARA. Results indicate that OTIs can be used to direct the sites of etoposide-induced DNA cleavage mediated by topoisomerase IIα and topoisomerase IIβ. OTIs increased levels of enzyme-mediated cleavage by inhibiting DNA ligation, and cleavage complexes induced by OTIs were as stable as those induced by free etoposide. Finally, OTIs directed against the PML-RARA breakpoint displayed cleavage specificity for oligonucleotides with the translocation sequence over those with sequences matching either parental gene. These studies demonstrate the feasibility of using oligonucleotides to direct topoisomerase II-mediated DNA cleavage to specific sites in the genome.
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MESH Headings
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Base Sequence
- DNA Cleavage/drug effects
- DNA Topoisomerases, Type II/metabolism
- Etoposide/chemistry
- Etoposide/pharmacology
- Feasibility Studies
- Humans
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Oncogene Proteins, Fusion/antagonists & inhibitors
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Topoisomerase II Inhibitors/chemistry
- Topoisomerase II Inhibitors/pharmacology
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Affiliation(s)
- Lorena Infante Lara
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Sabine Fenner
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Steven Ratcliffe
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Albert Isidro-Llobet
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Michael Hann
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
| | - Ben Bax
- Platform Technology and Science, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, 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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26
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Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα. Bioorg Med Chem Lett 2017; 27:4687-4693. [PMID: 28919339 DOI: 10.1016/j.bmcl.2017.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 01/03/2023]
Abstract
It has been proposed that xanthone derivatives with anticancer potential act as topoisomerase II inhibitors because they interfere with the ability of the enzyme to bind its ATP cofactor. In order to further characterize xanthone mechanism and generate compounds with potential as anticancer drugs, we synthesized a series of derivatives in which position 3 was substituted with different polyamine chains. As determined by DNA relaxation and decatenation assays, the resulting compounds are potent topoisomerase IIα inhibitors. Although xanthone derivatives inhibit topoisomerase IIα-catalyzed ATP hydrolysis, mechanistic studies indicate that they do not act at the ATPase site. Rather, they appear to function by blocking the ability of DNA to stimulate ATP hydrolysis. On the basis of activity, competition, and modeling studies, we propose that xanthones interact with the DNA cleavage/ligation active site of topoisomerase IIα and inhibit the catalytic activity of the enzyme by interfering with the DNA strand passage step.
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27
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Ashley RE, Lindsey RH, McPherson SA, Turnbough CL, Kerns RJ, Osheroff N. Interactions between Quinolones and Bacillus anthracis Gyrase and the Basis of Drug Resistance. Biochemistry 2017; 56:4191-4200. [PMID: 28708938 PMCID: PMC5560241 DOI: 10.1021/acs.biochem.7b00203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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Gyrase appears to
be the primary cellular target for quinolone
antibacterials in multiple pathogenic bacteria, including Bacillus anthracis, the causative agent of anthrax. Given
the significance of this type II topoisomerase as a drug target, it
is critical to understand how quinolones interact with gyrase and
how specific mutations lead to resistance. However, these important
issues have yet to be addressed for a canonical gyrase. Therefore,
we utilized a mechanistic approach to characterize interactions of
quinolones with wild-type B. anthracis gyrase and
enzymes containing the most common quinolone resistance mutations.
Results indicate that clinically relevant quinolones interact with
the enzyme through a water–metal ion bridge in which a noncatalytic
divalent metal ion is chelated by the C3/C4 keto acid of the drug.
In contrast to other bacterial type II topoisomerases that have been
examined, the bridge is anchored to gyrase primarily through a single
residue (Ser85). Substitution of groups at the quinolone C7 and C8
positions generated drugs that were less dependent on the water–metal
ion bridge and overcame resistance. Thus, by analyzing the interactions
of drugs with type II topoisomerases from individual bacteria, it
may be possible to identify specific quinolone derivatives that can
overcome target-mediated resistance in important pathogenic species.
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Affiliation(s)
| | | | - Sylvia A McPherson
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Charles L Turnbough
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Robert J Kerns
- Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa College of Pharmacy , Iowa City, Iowa 52242, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System , Nashville, Tennessee 37212, United States
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28
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Huang WC, Lee CY, Hsieh TS. Single-molecule Förster resonance energy transfer (FRET) analysis discloses the dynamics of the DNA-topoisomerase II (Top2) interaction in the presence of TOP2-targeting agents. J Biol Chem 2017. [PMID: 28630044 DOI: 10.1074/jbc.m117.792861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerases play crucial roles in DNA replication, transcription, and recombination. For instance, topoisomerase II (Top2) is critically important for resolving DNA tangles during cell division, and as such, it is a broad anticancer drug target. Top2 regulates DNA topology by transiently breaking one double-stranded DNA molecule (cleavage), allowing a second double strand to pass through the opened DNA gate (opening), and then closing the gate by rejoining the broken ends. Drugs that modulate Top2 catalysis may therefore affect enzymatic activity at several different steps. Previous studies have focused on examining DNA cleavage and ligation; however, the dynamic opening and closing of the DNA gate has been less explored. Here, we used the single-molecule Förster resonance energy transfer (smFRET) method to observe the open and closed state of the DNA gate and to measure dwell times in each state. Our results show that Top2 binds and bends DNA to increase the energy transfer efficiency (EFRET), and ATP treatment further induces the fluctuation of EFRET, representing the gate opening and closing. Additionally, our results demonstrate that both types of Top2-targeting anticancer drugs, the catalytic inhibitor dexrazoxane (ICRF187) and mechanistic poison teniposide (VM26), can interfere with DNA gate dynamics and shorten the dwell time in the closed state. Moreover, Top2 bound to the nonhydrolyzable ATP analog 5'-adenylyl-β,γ-imidodiphosphate exhibits altered DNA gate dynamics, but the DNA gate appears to open and close even after N-gate closure. In summary, we have utilized single-molecule detection to unravel Top2 DNA gate dynamics and reveal previously unknown effects of Top2 drugs on these dynamics.
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Affiliation(s)
- Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Chun-Ying Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Tao-Shih Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan; Department of Chemistry, National Taiwan University, Taipei 106, Taiwan; Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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29
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Mladenović M, Stanković N, Matić S, Stanić S, Mihailović M, Mihailović V, Katanić J, Boroja T, Vuković N. Newly discovered chroman-2,4-diones neutralize the in vivo DNA damage induced by alkylation through the inhibition of Topoisomerase IIα: A story behind the molecular modeling approach. Biochem Pharmacol 2015; 98:243-66. [PMID: 26319574 DOI: 10.1016/j.bcp.2015.08.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/24/2015] [Indexed: 01/09/2023]
Abstract
Eight chroman-2,4-diones, namely 2a-h, previously investigated as anticoagulants, of which 2a and 2f as the most active, were evaluated as in vivo genotoxic agents in Wistar rat livers and kidneys using the comet assay. Compounds 2a, 2b, and 2f without genotoxic activity were applied prior to ethyl methanesulfonate (EMS) and diminished EMS-induced DNA damage according to the total score and percentage of reduction. EMS produce harmful O(6)-ethylguanine lesion which is incorporated in aberrant genotoxic GT and TG pairing after ATP-dependent DNA strand breaks have been catalyzed by rat Topoisomerase IIα (rTopIIα, EC 5.99.1.3). Therefore, the mechanism of 2a, 2b, and 2f antigenotoxic activity was investigated on the enzyme level using molecular docking and molecular dynamics simulations insamuch as it had been determined that compounds do not intercalate DNA but instead inhibit the ATPase activity. Calculations predicted that compounds inhibit ATP hydrolysis before the DNA-EMS cleavage is being catalyzed by rTopIIα, prevent EMS mutagenic and carcinogenic effects, and beside anticoagulant activity can even be applied in the cancer treatment to control the rate of anticancer alkylation drugs.
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Affiliation(s)
- Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Nevena Stanković
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Sanja Matić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Snežana Stanić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Mirjana Mihailović
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia.
| | - Vladimir Mihailović
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Jelena Katanić
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Tatjana Boroja
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Nenad Vuković
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
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30
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Bisceglie F, Musiari A, Pinelli S, Alinovi R, Menozzi I, Polverini E, Tarasconi P, Tavone M, Pelosi G. Quinoline-2-carboxaldehyde thiosemicarbazones and their Cu(II) and Ni(II) complexes as topoisomerase IIa inhibitors. J Inorg Biochem 2015; 152:10-9. [PMID: 26335598 DOI: 10.1016/j.jinorgbio.2015.08.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/07/2015] [Accepted: 08/05/2015] [Indexed: 02/06/2023]
Abstract
A series of quinoline-2-carboxaldehyde thiosemicarbazones and their copper(II) and nickel(II) complexes were synthesized and characterized. In all complexes the ligands are in the E configuration with respect to the imino bond and behave as terdentate. The copper(II) complexes form square planar derivatives with one molecule of terdentate ligand and chloride ion. A further non-coordinated chloride ion compensates the overall charge. Nickel(II) ions form instead octahedral complexes with two ligands for each metal ion, independently from the stoichiometric metal:ligand ratio used in the synthesis. Ligands and complexes were tested for their antiproliferative properties on histiocytic lymphoma cell line U937. Copper(II) derivatives are systematically more active than the ligands and the nickel complexes. All copper derivatives result in inhibiting topoisomerase IIa in vitro. Computational methods were used to propose a model to explain the different extent of inhibition presented by these compounds. The positive charge of the dissociated form of the copper complexes may play a key role in their action.
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Affiliation(s)
- Franco Bisceglie
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy; CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), Parma Unit, University of Parma, Italy
| | - Anastasia Musiari
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Silvana Pinelli
- Department of Clinical and Experimental Medicine, University of Parma, Via Gramsci 14, 43126 Parma, Italy; CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), Parma Unit, University of Parma, Italy
| | - Rossella Alinovi
- Department of Clinical and Experimental Medicine, University of Parma, Via Gramsci 14, 43126 Parma, Italy; CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), Parma Unit, University of Parma, Italy
| | - Ilaria Menozzi
- Department of Physics and Earth Sciences, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Eugenia Polverini
- Department of Physics and Earth Sciences, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Pieralberto Tarasconi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy; CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), Parma Unit, University of Parma, Italy
| | - Matteo Tavone
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy
| | - Giorgio Pelosi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17A, 43124 Parma, Italy; CIRCMSB (Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici), Parma Unit, University of Parma, Italy.
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31
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Palermo G, Minniti E, Greco ML, Riccardi L, Simoni E, Convertino M, Marchetti C, Rosini M, Sissi C, Minarini A, De Vivo M. An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512. Chem Commun (Camb) 2015; 51:14310-3. [PMID: 26234198 DOI: 10.1039/c5cc05065k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combined computational-experimental analyses explain and quantify the spermine-vectorized F14512's boosted potency as a topoII poison. We found that an optimized polyamine moiety boosts drug binding to the topoII/DNA cleavage complex, rather than to the DNA alone. These results provide new structural bases and key reference data for designing new human topoII poisons.
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Affiliation(s)
- Giulia Palermo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy.
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32
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Lopata A, Jambrina PG, Sharma PK, Brooks BR, Toth J, Vertessy BG, Rosta E. Mutations Decouple Proton Transfer from Phosphate Cleavage in the dUTPase Catalytic Reaction. ACS Catal 2015. [DOI: 10.1021/cs502087f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Anna Lopata
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Pablo G. Jambrina
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Pankaz K. Sharma
- College
of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea
| | - Bernard R. Brooks
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892-9314, United States
| | - Judit Toth
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
| | - Beata G. Vertessy
- Institute
of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H1113, Hungary
- Department
of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest H1111, Hungary
| | - Edina Rosta
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
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33
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Drlica K, Mustaev A, Towle TR, Luan G, Kerns RJ, Berger JM. Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design. ACS Chem Biol 2014; 9:2895-904. [PMID: 25310082 PMCID: PMC4273985 DOI: 10.1021/cb500629k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Widespread
fluoroquinolone resistance has drawn attention to quinazolinediones
(diones), fluoroquinolone-like topoisomerase poisons that are unaffected
by common quinolone-resistance mutations. To better understand differences
between quinolones and diones, we examined their impact on the formation
of cleaved complexes (drug–topoisomerase–DNA complexes
in which the DNA moiety is broken) with gyrase, one of two bacterial
targets of the drugs. Formation of cleaved complexes, measured by
linearization of a circular DNA substrate, required lower concentrations
of quinolone than dione. The reverse reaction, detected as resealing
of DNA breaks in cleaved complexes, required higher temperatures and
EDTA concentrations for quinolones than diones. The greater stability
of quinolone-containing complexes was attributed to the unique ability
of the quinolone C3/C4 keto acid to complex with magnesium and form
a previously described drug–magnesium–water bridge with
GyrA-Ser83 and GyrA-Asp87. A nearby substitution in GyrA (G81C) reduced
activity differences between quinolone and dione, indicating that
resistance due to this variation derives from perturbation of the
magnesium–water bridge. To increase dione activity, we examined
a relatively small, flexible C-7-3-(aminomethyl)pyrrolidinyl substituent,
which is distal to the bridging C3/C4 keto acid substituent of quinolones.
The 3-(aminomethyl)pyrrolidinyl group at position C-7 was capable
of forming binding interactions with GyrB-Glu466, as indicated by
inspection of crystal structures, computer-aided docking, and measurement
of cleaved-complex formation with mutant and wild-type GyrB proteins.
Thus, modification of dione C-7 substituents constitutes a strategy
for obtaining compounds active against common quinolone-resistant
mutants.
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Affiliation(s)
- Karl Drlica
- Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Arkady Mustaev
- Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Tyrell R. Towle
- Division of Medicinal & Natural Products Chemistry, Department of Pharmaceutical Sciences & Experimental Therapeutics, University of Iowa College of Pharmacy, 115 South Grand Avenue, Iowa City, Iowa 52246, United States
| | - Gan Luan
- Public Health Research Institute and Department of Microbiology & Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Robert J. Kerns
- Division of Medicinal & Natural Products Chemistry, Department of Pharmaceutical Sciences & Experimental Therapeutics, University of Iowa College of Pharmacy, 115 South Grand Avenue, Iowa City, Iowa 52246, United States
| | - James M. Berger
- Molecular
and Cell Biology Department, Quantitative Biosciences Institute, University of California, Stanley Hall, Berkeley, California 94720, United States
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34
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Regal KM, Mercer SL, Deweese JE. HU-331 is a catalytic inhibitor of topoisomerase IIα. Chem Res Toxicol 2014; 27:2044-51. [PMID: 25409338 DOI: 10.1021/tx500245m] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Topoisomerases are essential enzymes that are involved in DNA metabolism. Topoisomerase II generates transient DNA strand breaks that are stabilized by anticancer drugs, such as doxorubicin, causing an accumulation of DNA damage. However, doxorubicin causes cardiac toxicity and, like etoposide and other topoisomerase II-targeted agents, can induce DNA damage, resulting in secondary cancers. The cannabinoid quinone HU-331 has been identified as a potential anticancer drug that demonstrates more potency in cancer cells with less off-target toxicity than that of doxorubicin. Reports indicate that HU-331 does not promote cell death via apoptosis, cell cycle arrest, caspase activation, or DNA strand breaks. However, the precise mechanism of action is poorly understood. We employed biochemical assays to study the mechanism of action of HU-331 against purified topoisomerase IIα. These assays examined DNA binding, cleavage, ligation, relaxation, and ATPase activities of topoisomerase IIα. Our results demonstrate that HU-331 inhibits topoisomerase IIα-mediated DNA relaxation at micromolar levels. We find that HU-331 does not induce DNA strand breaks in vitro. When added prior to the DNA substrate, HU-331 blocks DNA cleavage and relaxation activities of topoisomerase IIα in a redox-sensitive manner. The action of HU-331 can be blocked, but not reversed, by the presence of dithiothreitol. Our results also show that HU-331 inhibits the ATPase activity of topoisomerase IIα using a noncompetitive mechanism. Preliminary binding studies also indicate that HU-331 decreases the ability of topoisomerase IIα to bind DNA. In summary, HU-331 inhibits relaxation activity without poisoning DNA cleavage. This action is sensitive to reducing agents and appears to involve noncompetitive inhibition of the ATPase activity and possibly inhibition of DNA binding. These studies provide a promising foundation for the exploration of HU-331 as a catalytic inhibitor of topoisomerase IIα.
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Affiliation(s)
- Kellie M Regal
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences , Nashville, Tennessee 37204-3951, United States
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35
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Lindsey RH, Pendleton M, Ashley RE, Mercer SL, Deweese JE, Osheroff N. Catalytic core of human topoisomerase IIα: insights into enzyme-DNA interactions and drug mechanism. Biochemistry 2014; 53:6595-602. [PMID: 25280269 PMCID: PMC4204876 DOI: 10.1021/bi5010816] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Coordination between the N-terminal gate and the catalytic core of topoisomerase II allows the proper capture, cleavage, and transport of DNA during the catalytic cycle. Because the activities of these domains are tightly linked, it has been difficult to discern their individual contributions to enzyme-DNA interactions and drug mechanism. To further address the roles of these domains, we analyzed the activity of the catalytic core of human topoisomerase IIα. The catalytic core and the wild-type enzyme both maintained higher levels of cleavage with negatively (as compared to positively) supercoiled plasmid, indicating that the ability to distinguish supercoil handedness is embedded within the catalytic core. However, the catalytic core alone displayed little ability to cleave DNA substrates that did not intrinsically provide the enzyme with a transport segment (i.e., substrates that did not contain crossovers). Finally, in contrast to interfacial topoisomerase II poisons, covalent poisons did not enhance DNA cleavage mediated by the catalytic core. This distinction allowed us to further characterize the mechanism of etoposide quinone, a drug metabolite that functions primarily as a covalent poison. Etoposide quinone retained some ability to enhance DNA cleavage mediated by the catalytic core, indicating that it still can function as an interfacial poison. These results further define the distinct contributions of the N-terminal gate and the catalytic core to topoisomerase II function. The catalytic core senses the handedness of DNA supercoils during cleavage, while the N-terminal gate is critical for capturing the transport segment and for the activity of covalent poisons.
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Affiliation(s)
- R Hunter Lindsey
- Department of Biochemistry, ‡Department of Pharmacology, and §Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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36
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Abstract
OBJECTIVES Loop B is important for low-level quinolone resistance conferred by Qnr proteins. The role of individual amino acids within QnrS1 loop B in quinolone resistance and gyrase protection was assessed. METHODS qnrS1 and 11 qnrS1 alleles with site-directed Ala mutations in loop B were expressed in Escherichia coli BL21(DE3) and proteins were purified by affinity chromatography. Ciprofloxacin MICs were determined with and without IPTG. Gyrase DNA supercoiling was measured with and without ciprofloxacin IC50 and with various concentrations of QnrS1 proteins. RESULTS Wild-type QnrS1 and QnrS1 with Asn-110→Ala and Arg-111→Ala substitutions increased the ciprofloxacin MIC 12-fold in BL21(DE3), although QnrS1 with Gln-107→Ala replacement increased it 2-fold more than wild-type did. However, QnrS1 with Ala substitutions at His-106, Val-108, Ser-109, Met-112, Tyr-113, Phe-114, Cys-115 and Ser-116 increased ciprofloxacin MIC 1.4- to 8-fold less than wild-type QnrS1. Induction by 10-1000 μM IPTG increased ciprofloxacin MICs for all mutants, reaching values similar to those for wild-type. Purified wild-type and mutated proteins differed in protection of gyrase from ciprofloxacin action. Wild-type QnrS1 produced complete protection of gyrase supercoiling from ciprofloxacin (1.8 μM) action at 0.05 nM and half protection at 0.5 pM, whereas QnrS1 with Ala replacements that conferred the least increase in ciprofloxacin MICs also required the highest QnrS1 concentrations for protection. CONCLUSIONS Key individual residues in QnrS1 loop B affect ciprofloxacin resistance and gyrase protection from ciprofloxacin action, supporting the concept that loop B is key for interaction with gyrase necessary for quinolone resistance.
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Affiliation(s)
- María M Tavío
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA Microbiología, Departamento de Ciencias Clínicas, Universidad de Las Palmas de Gran Canaria, Las Palmas de G.C., España
| | | | - David C Hooper
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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37
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Abstract
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Quinolones
are one of the most commonly prescribed classes of antibacterials
in the world and are used to treat a variety of bacterial infections
in humans. Because of the wide use (and overuse) of these drugs, the
number of quinolone-resistant bacterial strains has been growing steadily
since the 1990s. As is the case with other antibacterial agents, the
rise in quinolone resistance threatens the clinical utility of this
important drug class. Quinolones act by converting their targets,
gyrase and topoisomerase IV, into toxic enzymes that fragment the
bacterial chromosome. This review describes the development of the
quinolones as antibacterials, the structure and function of gyrase
and topoisomerase IV, and the mechanistic basis for quinolone action
against their enzyme targets. It will then discuss the following three
mechanisms that decrease the sensitivity of bacterial cells to quinolones.
Target-mediated resistance is the most common and clinically significant
form of resistance. It is caused by specific mutations in gyrase and
topoisomerase IV that weaken interactions between quinolones and these
enzymes. Plasmid-mediated resistance results from extrachromosomal
elements that encode proteins that disrupt quinolone–enzyme
interactions, alter drug metabolism, or increase quinolone efflux.
Chromosome-mediated resistance results from the underexpression of
porins or the overexpression of cellular efflux pumps, both of which
decrease cellular concentrations of quinolones. Finally, this review
will discuss recent advancements in our understanding of how quinolones
interact with gyrase and topoisomerase IV and how mutations in these
enzymes cause resistance. These last findings suggest approaches to
designing new drugs that display improved activity against resistant
strains.
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Affiliation(s)
- Katie J Aldred
- Department of Biochemistry and ‡Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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38
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Ketron AC, Osheroff N. Phytochemicals as Anticancer and Chemopreventive Topoisomerase II Poisons. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2014; 13:19-35. [PMID: 24678287 PMCID: PMC3963363 DOI: 10.1007/s11101-013-9291-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phytochemicals are a rich source of anticancer drugs and chemopreventive agents. Several of these chemicals appear to exert at least some of their effects through interactions with topoisomerase II, an essential enzyme that regulates DNA supercoiling and removes knots and tangles from the genome. Topoisomerase II-active phytochemicals function by stabilizing covalent protein-cleaved DNA complexes that are intermediates in the catalytic cycle of the enzyme. As a result, these compounds convert topoisomerase II to a cellular toxin that fragments the genome. Because of their mode of action, they are referred to as topoisomerase II poisons as opposed to catalytic inhibitors. The first sections of this article discuss DNA topology, the catalytic cycle of topoisomerase II, and the two mechanisms (interfacial vs. covalent) by which different classes of topoisomerase II poisons alter enzyme activity. Subsequent sections discuss the effects of several phytochemicals on the type II enzyme, including demethyl-epipodophyllotoxins (semisynthetic anticancer drugs) as well as flavones, flavonols, isoflavones, catechins, isothiocyanates, and curcumin (dietary chemopreventive agents). Finally, the leukemogenic potential of topoisomerase II-targeted phytochemicals is described.
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Affiliation(s)
- Adam C. Ketron
- Department of Biochemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 USA
| | - Neil Osheroff
- Departments of Biochemistry and Medicine (Hematology/Oncology) and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 USA
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39
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Rosta E, Yang W, Hummer G. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. J Am Chem Soc 2014; 136:3137-44. [PMID: 24499076 PMCID: PMC3985467 DOI: 10.1021/ja411408x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 01/05/2023]
Abstract
Most phosphate-processing enzymes require Mg(2+) as a cofactor to catalyze nucleotide cleavage and transfer reactions. Ca(2+) ions inhibit many of these enzymatic activities, despite Ca(2+) and Mg(2+) having comparable binding affinities and overall biological abundances. Here we study the molecular details of the calcium inhibition mechanism for phosphodiester cleavage, an essential reaction in the metabolism of nucleic acids and nucleotides, by comparing Ca(2+)- and Mg(2+) catalyzed reactions. We study the functional roles of the specific metal ion sites A and B in enabling the catalytic cleavage of an RNA/DNA hybrid substrate by B. halodurans ribonuclease (RNase) H1 using hybrid quantum-mechanics/molecular mechanics (QM/MM) free energy calculations. We find that Ca(2+) substitution of either of the two active-site Mg(2+) ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity. Remarkably, Ca(2+) at the A site is inactive also in Mg(2+)-optimized active-site structures along the reaction path, whereas Mg(2+) substitution recovers activity in Ca(2+)-optimized structures. Geometric changes resulting from Ca(2+) substitution at metal ion site A may thus be a secondary factor in the loss of catalytic activity. By contrast, at metal ion site B geometry plays a more important role, with only a partial recovery of activity after Mg(2+) substitution in Ca(2+)-optimized structures. Ca(2+)-substitution also leads to a change in mechanism, with deprotonation of the water nucleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier. As a result, Ca(2+) is less efficient in activating the water. As a likely cause for the different reactivities of Mg(2+) and Ca(2+) ions in site A, we identify differences in charge transfer to the ions and the associated decrease in the pKa of the oxygen nucleophile attacking the phosphate group.
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Affiliation(s)
- Edina Rosta
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Wei Yang
- Laboratory
of Molecular Biology, National Institute
of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Gerhard Hummer
- Laboratory
of Chemical Physics, National Institute of
Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, 60438 Frankfurt am Main, Germany
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40
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Mustaev A, Malik M, Zhao X, Kurepina N, Luan G, Oppegard LM, Hiasa H, Marks KR, Kerns RJ, Berger JM, Drlica K. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding. J Biol Chem 2014; 289:12300-12. [PMID: 24497635 DOI: 10.1074/jbc.m113.529164] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys(466) gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly(81) and GyrB-Glu(466) residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases.
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Affiliation(s)
- Arkady Mustaev
- From the Public Health Research Institute and Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, New Jersey 07103
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41
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Pendleton M, Lindsey RH, Felix CA, Grimwade D, Osheroff N. Topoisomerase II and leukemia. Ann N Y Acad Sci 2014; 1310:98-110. [PMID: 24495080 DOI: 10.1111/nyas.12358] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Type II topoisomerases are essential enzymes that modulate DNA under- and overwinding, knotting, and tangling. Beyond their critical physiological functions, these enzymes are the targets for some of the most widely prescribed anticancer drugs (topoisomerase II poisons) in clinical use. Topoisomerase II poisons kill cells by increasing levels of covalent enzyme-cleaved DNA complexes that are normal reaction intermediates. Drugs such as etoposide, doxorubicin, and mitoxantrone are frontline therapies for a variety of solid tumors and hematological malignancies. Unfortunately, their use also is associated with the development of specific leukemias. Regimens that include etoposide or doxorubicin are linked to the occurrence of acute myeloid leukemias that feature rearrangements at chromosomal band 11q23. Similar rearrangements are seen in infant leukemias and are associated with gestational diets that are high in naturally occurring topoisomerase II-active compounds. Finally, regimens that include mitoxantrone and epirubicin are linked to acute promyelocytic leukemias that feature t(15;17) rearrangements. The first part of this article will focus on type II topoisomerases and describe the mechanism of enzyme and drug action. The second part will discuss how topoisomerase II poisons trigger chromosomal breaks that lead to leukemia and potential approaches for dissociating the actions of drugs from their leukemogenic potential.
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Affiliation(s)
- Maryjean Pendleton
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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42
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43
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Mayer C, Janin YL. Non-quinolone inhibitors of bacterial type IIA topoisomerases: a feat of bioisosterism. Chem Rev 2013; 114:2313-42. [PMID: 24313284 DOI: 10.1021/cr4003984] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Claudine Mayer
- Unité de Microbiologie Structurale, Département de Biologie Structurale et Chimie, Institut Pasteur , 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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44
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Hanaoka K, Shoji M, Kondo D, Sato A, Yang MY, Kamiya K, Shiraishi K. Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II. J Biomol Struct Dyn 2013; 32:1759-65. [PMID: 24047515 DOI: 10.1080/07391102.2013.834848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3' OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.
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Affiliation(s)
- Kyohei Hanaoka
- a Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba , 305-8571 , Japan
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45
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Arnoldi E, Pan XS, Fisher LM. Functional determinants of gate-DNA selection and cleavage by bacterial type II topoisomerases. Nucleic Acids Res 2013; 41:9411-23. [PMID: 23939623 PMCID: PMC3814380 DOI: 10.1093/nar/gkt696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Antibacterial fluoroquinolones trap a cleavage complex of gyrase and topoisomerase (topo) IV inducing site-specific DNA breakage within a bent DNA gate engaged in DNA transport. Despite its importance for drug action and in revealing potential sites of topoisomerase catalysis, the mechanism of DNA selectivity is poorly understood. To explore its functional basis, we generated mutant versions of the strongly cleaved E-site and used a novel competitive assay to examine their gemifloxacin-mediated DNA breakage by Streptococcus pneumoniae topo IV and gyrase. Parallel studies of Ca2+-induced cleavage distinguished ‘intrinsic recognition’ of DNA cleavage sites by topo IV from drug-induced preferences. Analysis revealed strong enzyme-determined requirements for −4G, −2A and −1T bases preceding the breakage site (between −1 and +1) and enzyme-unique or degenerate determinants at −3, plus drug-specific preferences at +2/+3 and for +1 purines associated with drug intercalation. Similar cleavage rules were seen additionally at the novel V-site identified here in ColE1-derived plasmids. In concert with DNA binding data, our results provide functional evidence for DNA, enzyme and drug contributions to DNA cleavage at the gate, suggest a mechanism for DNA discrimination involving enzyme-induced DNA bending/helix distortion and cleavage complex stabilization and advance understanding of fluoroquinolones as important cleavage-enhancing therapeutics.
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Affiliation(s)
- Elisa Arnoldi
- Division of Biomedical Sciences, St.George's, University of London, London SW17 0RE, UK
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46
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Sissi C, Cheng B, Lombardo V, Tse-Dinh YC, Palumbo M. Metal ion and inter-domain interactions as functional networks in E. coli topoisomerase I. Gene 2013; 524:253-60. [PMID: 23612251 DOI: 10.1016/j.gene.2013.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
Abstract
Escherichia coli topoisomerase I (EcTopoI) is a type IA bacterial topoisomerase which is receiving large attention due to its potential application as novel target for antibacterial therapeutics. Nevertheless, a detailed knowledge of its mechanism of action at molecular level is to some extent lacking. This is partly due to the requirement of several factors (metal ions, nucleic acid) to the proper progress of the enzyme catalytic cycle. Additionally, each of them can differently affect the protein structure. Here we assess the role of the different components (DNA, metal ions, protein domains) in a dynamic environment as in solution by monitoring the catalytic as well as the structural properties of EcTopoI. Our results clearly indicated the interaction among these components as functionally relevant and underlined their mutual involvement. Some similarities with other enzymes of the same family emerged (for example DNA prevents divalent metal ions coordination at non selective binding sites). Interestingly, same interactions (C- and N-terminal domain interaction) appear to be peculiar of this bacterial topoisomerase which suggest they could be favorably exploited to the design of selective inhibitors for this class of enzyme.
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Affiliation(s)
- Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, v. Marzolo 5, 35131 Padova, Italy.
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47
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Rao VA. Iron chelators with topoisomerase-inhibitory activity and their anticancer applications. Antioxid Redox Signal 2013; 18:930-55. [PMID: 22900902 PMCID: PMC3557438 DOI: 10.1089/ars.2012.4877] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
SIGNIFICANCE Iron and topoisomerases are abundant and essential cellular components. Iron is required for several key processes such as DNA synthesis, mitochondrial electron transport, synthesis of heme, and as a co-factor for many redox enzymes. Topoisomerases serve as critical enzymes that resolve topological problems during DNA synthesis, transcription, and repair. Neoplastic cells have higher uptake and utilization of iron, as well as elevated levels of topoisomerase family members. Separately, the chelation of iron and the cytotoxic inhibition of topoisomerase have yielded potent anticancer agents. RECENT ADVANCES The chemotherapeutic drugs doxorubicin and dexrazoxane both chelate iron and target topoisomerase 2 alpha (top2α). Newer chelators such as di-2-pyridylketone-4,4,-dimethyl-3-thiosemicarbazone and thiosemicarbazone -24 have recently been identified as top2α inhibitors. The growing list of agents that appear to chelate iron and inhibit topoisomerases prompts the question of whether and how these two distinct mechanisms might interplay for a cytotoxic chemotherapeutic outcome. CRITICAL ISSUES While iron chelation and topoisomerase inhibition each represent mechanistically advantageous anticancer therapeutic strategies, dual targeting agents present an attractive multi-modal opportunity for enhanced anticancer tumor killing and overcoming drug resistance. The commonalities and caveats of dual inhibition are presented in this review. FUTURE DIRECTIONS Gaps in knowledge, relevant biomarkers, and strategies for future in vivo studies with dual inhibitors are discussed.
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Affiliation(s)
- V Ashutosh Rao
- Laboratory of Biochemistry, Division of Therapeutic Proteins, Office of Biotechnology Products, Office of Pharmaceutical Science, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA.
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48
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Palermo G, Stenta M, Cavalli A, Dal Peraro M, De Vivo M. Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase. J Chem Theory Comput 2013; 9:857-62. [DOI: 10.1021/ct300691u] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Giulia Palermo
- Department of Drug Discovery
and Development, Italian Institute of Technology, via Morego 30, 16163
Genova, Italy
| | - Marco Stenta
- Institute
of Bioengineering,
School of Life Sciences, Ecole Polytechnique Fédérale
de Lausanne - EPFL, Lausanne, CH-1015, Switzerland
| | - Andrea Cavalli
- Department of Drug Discovery
and Development, Italian Institute of Technology, via Morego 30, 16163
Genova, Italy
- Department of Pharmaceutical Sciences,
University of Bologna, via Belmeloro 6, I-40126 Bologna, Italy
| | - Matteo Dal Peraro
- Institute
of Bioengineering,
School of Life Sciences, Ecole Polytechnique Fédérale
de Lausanne - EPFL, Lausanne, CH-1015, Switzerland
| | - Marco De Vivo
- Department of Drug Discovery
and Development, Italian Institute of Technology, via Morego 30, 16163
Genova, Italy
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49
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Vávrová A, Šimůnek T. DNA topoisomerase IIβ: a player in regulation of gene expression and cell differentiation. Int J Biochem Cell Biol 2012; 44:834-7. [PMID: 22465709 DOI: 10.1016/j.biocel.2012.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 01/06/2023]
Abstract
DNA topoisomerases II regulate conformational changes in DNA topology. They act on double-stranded DNA, catalyzing its relaxation, decatenation and unknotting. Vertebrate cells express two isoforms of topoisomerase II, which are similar in structure, but different in function and regulation. Whereas the alpha isoform is indispensable for proper cell replication, the functions of the beta isoform as well as reasons for its evolution in vertebrates were long unclear. Unlike topoisomerase II alpha, the beta isoform is predominantly expressed in quiescent cells and has been implicated mainly in the process of gene transcription. Recently, new discoveries point on the role of the topoisomerase II beta in regulation of cellular differentiation and tissue development. Furthermore, contemporary discoveries are raising possibilities for novel therapeutic approaches involving selective targeting of either topoisomerase II isoform in potentiating antitumor and/or reducing adverse effects of topoisomerase II poisons.
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Affiliation(s)
- Anna Vávrová
- Charles University in Prague, Faculty of Pharmacy in Hradec Králové, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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50
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DNA cleavage and opening reactions of human topoisomerase IIα are regulated via Mg2+-mediated dynamic bending of gate-DNA. Proc Natl Acad Sci U S A 2012; 109:2925-30. [PMID: 22323612 DOI: 10.1073/pnas.1115704109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Topoisomerase II resolves intrinsic topological problems of double-stranded DNA. As part of its essential cellular functions, the enzyme generates DNA breaks, but the regulation of this potentially dangerous process is not well understood. Here we report single-molecule fluorescence experiments that reveal a previously uncharacterized sequence of events during DNA cleavage by topoisomerase II: nonspecific DNA binding, sequence-specific DNA bending, and stochastic cleavage of DNA. We have identified unexpected structural roles of Mg(2+) ions coordinated in the TOPRIM (topoisomerase-primase) domain in inducing cleavage-competent DNA bending. A break at one scissile bond dramatically stabilized DNA bending, explaining how two scission events in opposing strands can be coordinated to achieve a high probability of double-stranded cleavage. Clamping of the protein N-gate greatly enhanced the rate and degree of DNA bending, resulting in a significant stimulation of the DNA cleavage and opening reactions. Our data strongly suggest that the accurate cleavage of DNA by topoisomerase II is regulated through a tight coordination with DNA bending.
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