151
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Yadav P, Owiti N, Kim N. The role of topoisomerase I in suppressing genome instability associated with a highly transcribed guanine-rich sequence is not restricted to preventing RNA:DNA hybrid accumulation. Nucleic Acids Res 2015; 44:718-29. [PMID: 26527723 PMCID: PMC4737143 DOI: 10.1093/nar/gkv1152] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 11/21/2022] Open
Abstract
Highly transcribed guanine-run containing sequences, in Saccharomyces cerevisiae, become unstable when topoisomerase I (Top1) is disrupted. Topological changes, such as the formation of extended RNA:DNA hybrids or R-loops or non-canonical DNA structures including G-quadruplexes has been proposed as the major underlying cause of the transcription-linked genome instability. Here, we report that R-loop accumulation at a guanine-rich sequence, which is capable of assembling into the four-stranded G4 DNA structure, is dependent on the level and the orientation of transcription. In the absence of Top1 or RNase Hs, R-loops accumulated to substantially higher extent when guanine-runs were located on the non-transcribed strand. This coincides with the orientation where higher genome instability was observed. However, we further report that there are significant differences between the disruption of RNase Hs and Top1 in regards to the orientation-specific elevation in genome instability at the guanine-rich sequence. Additionally, genome instability in Top1-deficient yeasts is not completely suppressed by removal of negative supercoils and further aggravated by expression of mutant Top1. Together, our data provide a strong support for a function of Top1 in suppressing genome instability at the guanine-run containing sequence that goes beyond preventing the transcription-associated RNA:DNA hybrid formation.
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Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Norah Owiti
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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152
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Vieira S, Castelli S, Desideri A. Importance of a stable topoisomerase IB clamping for an efficient DNA processing: Effect of the Lys 369 Glu mutation. Int J Biol Macromol 2015; 81:76-82. [DOI: 10.1016/j.ijbiomac.2015.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
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153
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Wallace BD, Williams RS. Ribonucleotide triggered DNA damage and RNA-DNA damage responses. RNA Biol 2015; 11:1340-6. [PMID: 25692233 DOI: 10.4161/15476286.2014.992283] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Research indicates that the transient contamination of DNA with ribonucleotides exceeds all other known types of DNA damage combined. The consequences of ribose incorporation into DNA, and the identity of protein factors operating in this RNA-DNA realm to protect genomic integrity from RNA-triggered events are emerging. Left unrepaired, the presence of ribonucleotides in genomic DNA impacts cellular proliferation and is associated with chromosome instability, gross chromosomal rearrangements, mutagenesis, and production of previously unrecognized forms of ribonucleotide-triggered DNA damage. Here, we highlight recent findings on the nature and structure of DNA damage arising from ribonucleotides in DNA, and the identification of cellular factors acting in an RNA-DNA damage response (RDDR) to counter RNA-triggered DNA damage.
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Affiliation(s)
- Bret D Wallace
- a Genome Integrity and Structural Biology Laboratory; National Institute of Environmental Health Sciences; NIH; DHHS ; Research Triangle Park , NC USA
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154
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Costa Pessoa J, Garribba E, Santos MF, Santos-Silva T. Vanadium and proteins: Uptake, transport, structure, activity and function. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.03.016] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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155
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Naumczuk B, Hyz K, Kawęcki R, Bocian W, Bednarek E, Sitkowski J, Wielgus E, Kozerski L. DOSY NMR and MALDI-TOF evidence of covalent binding the DNA duplex by trimethylammonium salts of topotecan upon near UV irradiation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:565-571. [PMID: 26017759 DOI: 10.1002/mrc.4255] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/25/2015] [Accepted: 04/01/2015] [Indexed: 06/04/2023]
Abstract
Using DOSY NMR and MALDI-TOF MS techniques, we present evidence that quaternary trimethylammonium salts of topotecan, [TPT-NMe3 ](+) X(-) (X = CF3SO3, HCOO), bind covalently the natural DNA oligomer upon near UV irradiation in water under physiological conditions. It is shown that formate salt is very reactive at pH 7 and requires short irradiation time. This weak irradiation at 365 nm paves the way for a new application of TPT derivatives in clinical use, which can dramatically increase the therapeutic effects of a medicine.
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Affiliation(s)
- Beata Naumczuk
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
| | - Karolina Hyz
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
| | - Robert Kawęcki
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
- University of Natural Sciences and Humanities, 80-110, Siedlce, Poland
| | - Wojciech Bocian
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
- National Medicines Institute, 00-725, Warsaw, Chełmska 30/34, Poland
| | - Elżbieta Bednarek
- National Medicines Institute, 00-725, Warsaw, Chełmska 30/34, Poland
| | - Jerzy Sitkowski
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
- National Medicines Institute, 00-725, Warsaw, Chełmska 30/34, Poland
| | - Ewelina Wielgus
- Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | - Lech Kozerski
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Kasprzaka 44, Poland
- National Medicines Institute, 00-725, Warsaw, Chełmska 30/34, Poland
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156
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Xu Y, Her C. Inhibition of Topoisomerase (DNA) I (TOP1): DNA Damage Repair and Anticancer Therapy. Biomolecules 2015; 5:1652-70. [PMID: 26287259 PMCID: PMC4598769 DOI: 10.3390/biom5031652] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/14/2015] [Indexed: 12/31/2022] Open
Abstract
Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained proliferation is a common feature of cancer [1,2]. Rapid DNA replication is essential for highly proliferative cells, thus blocking of DNA replication will create numerous mutations and/or chromosome rearrangements—ultimately triggering cell death [3]. Along these lines, DNA topoisomerase inhibitors are of great interest because they help to maintain strand breaks generated by topoisomerases during replication. In this article, we discuss the characteristics of topoisomerase (DNA) I (TOP1) and its inhibitors, as well as the underlying DNA repair pathways and the use of TOP1 inhibitors in cancer therapy.
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Affiliation(s)
- Yang Xu
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA.
| | - Chengtao Her
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA.
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157
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Sulfonoquinovosyl diacylglyceride selectively targets acute lymphoblastic leukemia cells and exerts potent anti-leukemic effects in vivo. Sci Rep 2015; 5:12082. [PMID: 26189912 PMCID: PMC4507174 DOI: 10.1038/srep12082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 06/08/2015] [Indexed: 11/22/2022] Open
Abstract
DNA topoisomerase II inhibitors e.g. doxorubicin and etoposide are currently
used in the chemotherapy for acute lymphoblastic leukemia (ALL). These inhibitors
have serious side effects during the chemotherapy e.g. cardiotoxicity and
secondary malignancies. In this study we show that sulfonoquinovosyl diacylglyceride
(SQDG) isolated from Azadirachta indica exerts potent anti-ALL activity both
in vitro and in vivo in nude mice and it synergizes with
doxorubicin and etoposide. SQDG selectively targets ALL MOLT-4 cells by inhibiting
catalytic activity of topoisomerase I enzyme and inducing p53 dependent apoptotic
pathway. SQDG treatment induces recruitment of ATR at chromatin and arrests the
cells in S-phase. Down-regulation of topoisomerase I or p53 renders the cells less
sensitive for SQDG, while ectopic expression of wild type p53 protein in p53
deficient K562 cells results in chemosensitization of the cells for SQDG. We also
show that constant ratio combinations of SQDG and etoposide or SDQG and doxorubicin
exert synergistic effects on MOLT-4 cell killing. This study suggests that doses of
etoposide/doxorubicin can be substantially reduced by combining SQDG with these
agents during ALL chemotherapy and side effects caused can be minimized. Thus dual
targeting of topoisomerase I and II enzymes is a promising strategy for improving
ALL chemotherapy.
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158
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Huang NL, Lin JH. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation. Nucleic Acids Res 2015; 43:6772-86. [PMID: 26150421 PMCID: PMC4538842 DOI: 10.1093/nar/gkv672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/19/2015] [Indexed: 01/24/2023] Open
Abstract
Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.
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Affiliation(s)
- Nan-Lan Huang
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan Institute of Biomedical Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan School of Pharmacy, National Taiwan University, Taipei 10050, Taiwan
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159
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Shen Y, Aoyagi-Scharber M, Wang B. Trapping Poly(ADP-Ribose) Polymerase. J Pharmacol Exp Ther 2015; 353:446-57. [PMID: 25758918 DOI: 10.1124/jpet.114.222448] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/09/2015] [Indexed: 03/08/2025] Open
Abstract
Recent findings indicate that a major mechanism by which poly(ADP-ribose) polymerase (PARP) inhibitors kill cancer cells is by trapping PARP1 and PARP2 to the sites of DNA damage. The PARP enzyme-inhibitor complex "locks" onto damaged DNA and prevents DNA repair, replication, and transcription, leading to cell death. Several clinical-stage PARP inhibitors, including veliparib, rucaparib, olaparib, niraparib, and talazoparib, have been evaluated for their PARP-trapping activity. Although they display similar capacity to inhibit PARP catalytic activity, their relative abilities to trap PARP differ by several orders of magnitude, with the ability to trap PARP closely correlating with each drug's ability to kill cancer cells. In this article, we review the available data on molecular interactions between these clinical-stage PARP inhibitors and PARP proteins, and discuss how their biologic differences might be explained by the trapping mechanism. We also discuss how to use the PARP-trapping mechanism to guide the development of PARP inhibitors as a new class of cancer therapy, both for single-agent and combination treatments.
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Affiliation(s)
- Yuqiao Shen
- BioMarin Pharmaceutical Inc., Novato, California
| | | | - Bing Wang
- BioMarin Pharmaceutical Inc., Novato, California
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160
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Salvio R. The guanidinium unit in the catalysis of phosphoryl transfer reactions: from molecular spacers to nanostructured supports. Chemistry 2015; 21:10960-71. [PMID: 25940903 DOI: 10.1002/chem.201500789] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Examples of guanidinium-based artificial phosphodiesterases are illustrated in this review article. A wide set of collected catalytic systems are presented, from the early examples to the most recent developments of the use of this unit in the design of supramolecular catalysts. Special attention is dedicated to illustrate the operating catalytic mechanism and the role of guanidine/ium units in the catalysis. One or more of these units can act by themselves or in conjunction with other active units. The analogy with the mechanism of enzymatic systems is presented and discussed. In the last part of this overview, recent examples of guanidinophosphodiesterases based on nanostructured supports are reported, namely gold-monolayer-protected clusters and polymer brushes grafted to silica nanoparticles. The issue of the dependence of the catalytic performance on the preorganization of the spacer is tackled and discussed in terms of effective molarity, a parameter that can be taken as a quantitative measurement of this preorganization for both conventional molecular linker and nanosized supports.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Chimica and IMC-CNR, Sezione Meccanismi di Reazione, La Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 (Italy).
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161
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Sirikantaramas S, Meeprasert A, Rungrotmongkol T, Fuji H, Hoshino T, Sudo H, Yamazaki M, Saito K. Structural insight of DNA topoisomerases I from camptothecin-producing plants revealed by molecular dynamics simulations. PHYTOCHEMISTRY 2015; 113:50-56. [PMID: 25733498 DOI: 10.1016/j.phytochem.2015.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 12/23/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
DNA topoisomerase I (Top1) catalyzes changes in DNA topology by cleaving and rejoining one strand of the double stranded (ds)DNA. Eukaryotic Top1s are the cellular target of the plant-derived anticancer indole alkaloid camptothecin (CPT), which reversibly stabilizes the Top1-dsDNA complex. However, CPT-producing plants, including Camptotheca acuminata, Ophiorrhiza pumila and Ophiorrhiza liukiuensis, are highly resistant to CPT because they possess point-mutated Top1. Here, the adaptive convergent evolution is reported between CPT production ability and mutations in their Top1, as a universal resistance mechanism found in all tested CPT-producing plants. This includes Nothapodytes nimmoniana, one of the major sources of CPT. To obtain a structural insight of the resistance mechanism, molecular dynamics simulations of CPT- resistant and -sensitive plant Top1s complexed with dsDNA and topotecan (a CPT derivative) were performed, these being compared to that for the CPT-sensitive human Top1. As a result, two mutations, Val617Gly and Asp710Gly, were identified in O. pumila Top1 and C. acuminata Top1, respectively. The substitutions at these two positions, surprisingly, are the same as those found in a CPT derivative-resistant human colon adenocarcinoma cell line. The results also demonstrated an increased linker flexibility of the CPT-resistant Top1, providing an additional explanation for the resistance mechanism found in CPT-producing plants. These mutations could reflect the long evolutionary adaptation of CPT-producing plant Top1s to confer a higher degree of resistance.
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Affiliation(s)
- Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Thailand; Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Japan.
| | - Arthitaya Meeprasert
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Thailand
| | | | - Hideyoshi Fuji
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Tyuji Hoshino
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Hiroshi Sudo
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Japan; Faculty of Pharmaceutical Sciences, Hoshi University, Japan
| | - Mami Yamazaki
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Japan
| | - Kazuki Saito
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Japan.
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162
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Ataei S, Yilmaz S, Ertan-Bolelli T, Yildiz I. Generated 3D-common feature hypotheses using the HipHop method for developing new topoisomerase I inhibitors. Arch Pharm (Weinheim) 2015; 348:498-507. [PMID: 25914208 DOI: 10.1002/ardp.201500045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/15/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022]
Abstract
The continued interest in designing novel topoisomerase I (Topo I) inhibitors and the lack of adequate ligand-based computer-aided drug discovery efforts combined with the drawbacks of structure-based design prompted us to explore the possibility of developing ligand-based three-dimensional (3D) pharmacophore(s). This approach avoids the pitfalls of structure-based techniques because it only focuses on common features among known ligands; furthermore, the pharmacophore model can be used as 3D search queries to discover new Topo I inhibitory scaffolds. In this article, we employed the HipHop module using Discovery Studio to construct plausible binding hypotheses for clinically used Topo I inhibitors, such as camptothecin, topotecan, belotecan, and SN-38, which is an active metabolite of irinotecan. The docked pose of topotecan was selected as a reference compound. The first hypothesis (Hypo 01) among the obtained 10 hypotheses was chosen for further analysis. Hypo 01 had six features, which were two hydrogen-bond acceptors, one hydrogen-bond donor, one hydrophob aromatic and one hydrophob aliphatic, and one ring aromatic. Our obtained hypothesis was checked by using some of the aromathecin derivatives which were published for their Topo I inhibitory potency. Moreover, five structures were found to be possible anti-Topo I compounds from the DruglikeDiverse database. From this research, it can be suggested that our model could be useful for further studies in order to design new potent Topo I-targeting antitumor drugs.
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Affiliation(s)
- Sanaz Ataei
- Biotechnology Institute, Ankara University, Tandogan-Ankara, Turkey
| | - Serap Yilmaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Turkey
| | - Tugba Ertan-Bolelli
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Turkey
| | - Ilkay Yildiz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Turkey
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163
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Wang Z, D'Annessa I, Tesauro C, Croce S, Ottaviani A, Fiorani P, Desideri A. Mutation of Gly717Phe in human topoisomerase 1B has an effect on enzymatic function, reactivity to the camptothecin anticancer drug and on the linker domain orientation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:860-8. [PMID: 25910424 DOI: 10.1016/j.bbapap.2015.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
Abstract
Human topoisomerase 1B controls the topological state of supercoiled DNA allowing the progression of fundamental cellular processes. The enzyme, which is the unique molecular target of the natural anticancer compound camptothecin, acts by cleaving one DNA strand and forming a transient protein-DNA covalent adduct. In this work the role of the Gly717 residue, located in a α-helix structure bridging the active site and the linker domain, has been investigated mutating it in Phe. The mutation gives rise to drug resistance in vivo as observed through a viability assay of yeast cells. In vitro activity assays show that the mutant is characterized by a fast religation rate, only partially reduced by the presence of the drug. Comparative molecular dynamics simulations of the native and mutant proteins indicate that the mutation of Gly717 affects the motion orientation of the linker domain, changing its interaction with the DNA substrate, likely affecting the strand rotation and religation rate. The mutation also causes a slight rearrangement of the active site and of the drug binding site, providing an additional explanation for the lowered effect of camptothecin toward the mutant.
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Affiliation(s)
- Zhenxing Wang
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Ilda D'Annessa
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Stefano Croce
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, 00133 Rome, Italy.
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
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164
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Huang SYN, Ghosh S, Pommier Y. Topoisomerase I alone is sufficient to produce short DNA deletions and can also reverse nicks at ribonucleotide sites. J Biol Chem 2015; 290:14068-76. [PMID: 25887397 DOI: 10.1074/jbc.m115.653345] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide monophosphates (rNMPs) are among the most frequent form of DNA aberration, as high ratios of ribonucleotide triphosphate:deoxyribonucleotide triphosphate pools result in approximately two misincorporated rNMPs/kb of DNA. The main pathway for the removal of rNMPs is by RNase H2. However, in a RNase H2 knock-out yeast strain, a topoisomerase I (Top1)-dependent mutator effect develops with accumulation of short deletions within tandem repeats. Proposed models for these deletions implicated processing of Top1-generated nicks at rNMP sites and/or sequential Top1 binding, but experimental support has been lacking thus far. Here, we investigated the biochemical mechanism of the Top1-induced short deletions at the rNMP sites by generating nicked DNA substrates bearing 2',3'-cyclic phosphates at the nick sites, mimicking the Top1-induced nicks. We demonstrate that a second Top1 cleavage complex adjacent to the nick and subsequent faulty Top1 religation led to the short deletions. Moreover, when acting on the nicked DNA substrates containing 2',3'-cyclic phosphates, Top1 generated not only the short deletion, but also a full-length religated DNA product. A catalytically inactive Top1 mutant (Top1-Y723F) also induced the full-length products, indicating that Top1 binding independent of its enzymatic activity promotes the sealing of DNA backbones via nucleophilic attacks by the 5'-hydroxyl on the 2',3'-cyclic phosphate. The resealed DNA would allow renewed attempt for repair by the error-free RNase H2-dependent pathway in vivo. Our results provide direct evidence for the generation of short deletions by sequential Top1 cleavage events and for the promotion of nick religation at rNMP sites by Top1.
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Affiliation(s)
- Shar-Yin Naomi Huang
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Sanchari Ghosh
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yves Pommier
- From the Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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165
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Wright CM, van der Merwe M, DeBrot AH, Bjornsti MA. DNA topoisomerase I domain interactions impact enzyme activity and sensitivity to camptothecin. J Biol Chem 2015; 290:12068-78. [PMID: 25795777 DOI: 10.1074/jbc.m114.635078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 11/06/2022] Open
Abstract
During processes such as DNA replication and transcription, DNA topoisomerase I (Top1) catalyzes the relaxation of DNA supercoils. The nuclear enzyme is also the cellular target of camptothecin (CPT) chemotherapeutics. Top1 contains four domains: the highly conserved core and C-terminal domains involved in catalysis, a coiled-coil linker domain of variable length, and a poorly conserved N-terminal domain. Yeast and human Top1 share a common reaction mechanism and domain structure. However, the human Top1 is ∼100-fold more sensitive to CPT. Moreover, substitutions of a conserved Gly(717) residue, which alter intrinsic enzyme sensitivity to CPT, induce distinct phenotypes in yeast. To address the structural basis for these differences, reciprocal swaps of yeast and human Top1 domains were engineered in chimeric enzymes. Here we report that intrinsic Top1 sensitivity to CPT is dictated by the composition of the conserved core and C-terminal domains. However, independent of CPT, biochemically similar chimeric enzymes produced strikingly distinct phenotypes in yeast. Expression of a human Top1 chimera containing the yeast linker domain proved toxic, even in the context of a catalytically inactive Y723F enzyme. Lethality was suppressed either by splicing the yeast N-terminal domain into the chimera, deleting the human N-terminal residues, or in enzymes reconstituted by polypeptide complementation. These data demonstrate a functional interaction between the N-terminal and linker domains, which, when mispaired between yeast and human enzymes, induces cell lethality. Because toxicity was independent of enzyme catalysis, the inappropriate coordination of N-terminal and linker domains may induce aberrant Top1-protein interactions to impair cell growth.
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Affiliation(s)
- Christine M Wright
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Marié van der Merwe
- Department of Molecular Pharmacology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Amanda H DeBrot
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
| | - Mary-Ann Bjornsti
- From the Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294 and
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166
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Vieira S, Castelli S, Falconi M, Takarada J, Fiorillo G, Buzzetti F, Lombardi P, Desideri A. Role of 13-(di)phenylalkyl berberine derivatives in the modulation of the activity of human topoisomerase IB. Int J Biol Macromol 2015; 77:68-75. [PMID: 25783020 DOI: 10.1016/j.ijbiomac.2015.02.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/26/2015] [Accepted: 02/28/2015] [Indexed: 12/25/2022]
Abstract
Topoisomerases IB are anticancer and antimicrobial targets whose inhibition by several natural and non-natural compounds has been documented. The inhibition effect by berberine and some 13-(di)phenylalkyl berberine derivatives has been tested towards human topoisomerase IB. Derivatives belonging to the 13-diphenylalkyl series display an efficient inhibition of the DNA relaxation and cleavage step, that increases upon pre-incubation with the enzyme. The religation step of the enzyme catalytic cycle is not affected by compounds and only slightly upon pre-incubation. The binding of the protein to the DNA substrate occurs also in the presence of the compounds, as monitored by a DNA shift assay, indicating that the compounds are not able to inhibit the formation of the enzyme-DNA complex but that they act as catalytic inhibitors.
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Affiliation(s)
- Sara Vieira
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy
| | - Silvia Castelli
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy
| | - Mattia Falconi
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy
| | - Jéssica Takarada
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy
| | - Gaetano Fiorillo
- Naxospharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese, Italy
| | - Franco Buzzetti
- Naxospharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese, Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio, 70, 20026 Novate Milanese, Italy
| | - Alessandro Desideri
- University of Rome Tor Vergata, Department of Biology, Via Della Ricerca Scientifica, 00133 Rome, Italy.
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167
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Cyclane-aminol 10-hydroxycamptothecin analogs as novel DNA topoisomerase I inhibitors induce apoptosis selectively in tumor cells. Anticancer Drugs 2015; 25:614-23. [PMID: 24525588 DOI: 10.1097/cad.0000000000000083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A novel series of cyclane-aminol 10-hydroxycamptothecin (HCPT) analogs was designed and synthesized through the Mannich reaction using HCPT as the lead compound, such as 10-hydroxyl-9-L-prolinol (+) methylcamptothecin (PRPT), 10-hydroxyl-9-(4'-hydroxy) piperidinylmethylcamptothecin (PPPT), and 10-hydroxy-9-(4'-hydroxyethyl)-piperazinylmethycamptothecin (QPPT). Three kinds of new cyclane-aminols were introduced into the structure of HCPT, which modified strong cytotoxic HCPT into cyclane-aminol HCPT analogs with moderate cytotoxicity and improved selectivity toward DNA topoisomerase I inhibition in tumor cells. Special metabolic pathways for cyclane-aminol HCPT analogs in rats were discovered, which differed from other HCPT analogs. Cyclane-aminol HCPT analogs can capture O2 and cause an increase in intracellular hydrogen peroxide levels with selective induction of apoptosis in tumor cells rather than in normal peripheral blood mononuclear cells. Among them, PPPT has a much better druggability than topotecan (TPT) and has the potential to be developed into an antitumor agent.
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168
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Lin RW, Yang CN, Ku S, Ho CJ, Huang SB, Yang MC, Chang HW, Lin CM, Hwang J, Chen YL, Tzeng CC, Wang C. CFS-1686 causes cell cycle arrest at intra-S phase by interference of interaction of topoisomerase 1 with DNA. PLoS One 2014; 9:e113832. [PMID: 25460368 PMCID: PMC4252032 DOI: 10.1371/journal.pone.0113832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/30/2014] [Indexed: 01/07/2023] Open
Abstract
CFS-1686 (chemical name (E)-N-(2-(diethylamino)ethyl)-4-(2-(2-(5-nitrofuran-2-yl)vinyl)quinolin-4-ylamino)benzamide) inhibits cell proliferation and triggers late apoptosis in prostate cancer cell lines. Comparing the effect of CFS-1686 on cell cycle progression with the topoisomerase 1 inhibitor camptothecin revealed that CFS-1686 and camptothecin reduced DNA synthesis in S-phase, resulting in cell cycle arrest at the intra-S phase and G1-S boundary, respectively. The DNA damage in CFS-1686 and camptothecin treated cells was evaluated by the level of ATM phosphorylation, γH2AX, and γH2AX foci, showing that camptothecin was more effective than CFS-1686. However, despite its lower DNA damage capacity, CFS-1686 demonstrated 4-fold higher inhibition of topoisomerase 1 than camptothecin in a DNA relaxation assay. Unlike camptothecin, CFS-1686 demonstrated no activity on topoisomerase 1 in a DNA cleavage assay, but nevertheless it reduced the camptothecin-induced DNA cleavage of topoisomerase 1 in a dose-dependent manner. Our results indicate that CFS-1686 might bind to topoisomerase 1 to inhibit this enzyme from interacting with DNA relaxation activity, unlike campothecin's induction of a topoisomerase 1-DNA cleavage complex. Finally, we used a computer docking strategy to localize the potential binding site of CFS-1686 to topoisomerase 1, further indicating that CFS-1686 might inhibit the binding of Top1 to DNA.
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Affiliation(s)
- Ru-Wei Lin
- Bone and Joint Research Center, National Cheng Kung University, Tainan, Taiwan
- Medical Device R & D Core Laboratory, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Chia-Ning Yang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - ShengYu Ku
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cheng-Jung Ho
- Department of Orthopedics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shih-Bo Huang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Min-Chi Yang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Wen Chang
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Chun-Mao Lin
- Department of Biochemistry, School of Medical, Taipei Medical University, Taipei, Taiwan
| | - Jaulang Hwang
- Department of Biochemistry, School of Medical, Taipei Medical University, Taipei, Taiwan
| | - Yeh-Long Chen
- Department of Medical and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cherg-Chyi Tzeng
- Department of Medical and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chihuei Wang
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
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169
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Comeaux EQ, van Waardenburg RCAM. Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target. Drug Metab Rev 2014; 46:494-507. [PMID: 25327705 DOI: 10.3109/03602532.2014.971957] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target.
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Affiliation(s)
- Evan Q Comeaux
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham , Birmingham, AL , USA
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170
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Miller JM, Arachea BT, Epling LB, Enemark EJ. Analysis of the crystal structure of an active MCM hexamer. eLife 2014; 3:e03433. [PMID: 25262915 PMCID: PMC4359371 DOI: 10.7554/elife.03433] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/28/2014] [Indexed: 12/26/2022] Open
Abstract
In a previous Research article (Froelich et al., 2014), we suggested an MCM helicase activation mechanism, but were limited in discussing the ATPase domain because it was absent from the crystal structure. Here we present the crystal structure of a nearly full-length MCM hexamer that is helicase-active and thus has all features essential for unwinding DNA. The structure is a chimera of Sulfolobus solfataricus N-terminal domain and Pyrococcus furiosus ATPase domain. We discuss three major findings: 1) a novel conformation for the A-subdomain that could play a role in MCM regulation; 2) interaction of a universally conserved glutamine in the N-terminal Allosteric Communication Loop with the AAA+ domain helix-2-insert (h2i); and 3) a recessed binding pocket for the MCM ssDNA-binding motif influenced by the h2i. We suggest that during helicase activation, the h2i clamps down on the leading strand to facilitate strand retention and regulate ATP hydrolysis. DOI:http://dx.doi.org/10.7554/eLife.03433.001
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Affiliation(s)
- Justin M Miller
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Buenafe T Arachea
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, United States
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171
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Wan JP, Zhou Y, Cao S. Domino Reactions Involving the Branched C–N and C═C Cleavage of Enaminones Toward Pyridines Synthesis. J Org Chem 2014; 79:9872-7. [DOI: 10.1021/jo5018266] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jie-Ping Wan
- Key Laboratory of Functional
Small Organic Molecules, Ministry of Education and College of Chemistry
and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Youyi Zhou
- Key Laboratory of Functional
Small Organic Molecules, Ministry of Education and College of Chemistry
and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China
| | - Shuo Cao
- Key Laboratory of Functional
Small Organic Molecules, Ministry of Education and College of Chemistry
and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China
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172
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Biophysical highlights from 54 years of macromolecular crystallography. Biophys J 2014; 106:510-25. [PMID: 24507592 DOI: 10.1016/j.bpj.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/03/2014] [Indexed: 12/22/2022] Open
Abstract
The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the first excitement of the myoglobin and hemoglobin structures in 1960. Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure.
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173
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Tesauro C, Graziani G, Arnò B, Zuccaro L, Muzi A, D'Annessa I, Santori E, Tentori L, Leonetti C, Fiorani P, Desideri A. Mutations of human DNA topoisomerase I at poly(ADP-ribose) binding sites: modulation of camptothecin activity by ADP-ribose polymers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:71. [PMID: 25227992 PMCID: PMC4172901 DOI: 10.1186/s13046-014-0071-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/19/2014] [Indexed: 12/02/2022]
Abstract
Background DNA topoisomerases are key enzymes that modulate the topological state of DNA through the breaking and rejoining of DNA strands. Human topoisomerase I belongs to the family of poly(ADP-ribose)-binding proteins and is the target of camptothecin derived anticancer drugs. Poly(ADP-ribosyl)ation occurs at specific sites of the enzyme inhibiting the cleavage and enhancing the religation steps during the catalytic cycle. Thus, ADP-ribose polymers antagonize the activity of topoisomerase I poisons, whereas PARP inhibitors increase their antitumor effects. Methods Using site-directed mutagenesis we have analyzed the interaction of human topoisomerase I and poly(ADP-ribose) through enzymatic activity and binding procedures. Results Mutations of the human topoisomerase I hydrophobic or charged residues, located on the putative polymer binding sites, are not sufficient to abolish or reduce the binding of the poly(ADP-ribose) to the protein. These results suggest either the presence of additional binding sites or that the mutations are not enough perturbative to destroy the poly(ADP-ribose) interaction, although in one mutant they fully abolish the enzyme activity. Conclusions It can be concluded that mutations at the hydrophobic or charged residues of the putative polymer binding sites do not interfere with the ability of poly(ADP-ribose) to antagonize the antitumor activity of topoisomerase I poisons.
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174
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Sangani CB, Makawana JA, Duan YT, Yin Y, Teraiya SB, Thumar NJ, Zhu HL. Design, synthesis and molecular modeling of biquinoline–pyridine hybrids as a new class of potential EGFR and HER-2 kinase inhibitors. Bioorg Med Chem Lett 2014; 24:4472-4476. [DOI: 10.1016/j.bmcl.2014.07.094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/29/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
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175
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Rajan R, Osterman AK, Gast AT, Mondragón A. Biochemical characterization of the topoisomerase domain of Methanopyrus kandleri topoisomerase V. J Biol Chem 2014; 289:28898-909. [PMID: 25135643 DOI: 10.1074/jbc.m114.590711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Topoisomerases are ubiquitous enzymes that modify the topological state of DNA inside the cell and are essential for several cellular processes. Topoisomerase V is the sole member of the type IC topoisomerase subtype. The topoisomerase domain has a unique fold among topoisomerases, and the putative active site residues show a distinct arrangement. The present study was aimed at identifying the roles of the putative active site residues in the DNA cleavage/religation process. Residues Arg-131, Arg-144, His-200, Glu-215, Lys-218, and Tyr-226 were mutated individually to a series of conservative and non-conservative amino acids, and the DNA relaxation activity at different pH values, times, and enzyme concentrations was compared with wild-type activity. The results suggest that Arg-144 is essential for protein stability because any substitution at this position was deleterious and that Arg-131 and His-200 are involved in transition state stabilization. Glu-215 reduces the DNA binding ability of topoisomerase V, especially in shorter fragments with fewer helix-hairpin-helix DNA binding motifs. Finally, Lys-218 appears to play a direct role in catalysis but not in charge stabilization of the protein-DNA intermediate complex. The results suggest that although catalytically important residues are oriented in different fashions in the active sites of type IB and type IC topoisomerases, similar amino acids play equivalent roles in both of these subtypes of enzymes, showing convergent evolution of the catalytic mechanism.
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Affiliation(s)
- Rakhi Rajan
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Amy K Osterman
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Alexandra T Gast
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Alfonso Mondragón
- From the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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176
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Katkar P, Coletta A, Castelli S, Sabino GL, Couto RAA, Ferreira AMDC, Desideri A. Effect of oxindolimine copper(II) and zinc(II) complexes on human topoisomerase I activity. Metallomics 2014; 6:117-25. [PMID: 24172750 DOI: 10.1039/c3mt00099k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability of oxindolimine copper(II) and zinc(II) complexes, known to have antitumor activity, to inhibit human topoisomerase IB has been tested through enzymatic kinetic assays and molecular docking simulations. These copper and zinc compounds are able to inhibit remarkably the cleavage reaction and only partially the religation step, the copper compound being more efficient than the zinc one. A complete inhibition activity of the cleavage is only obtained when the enzyme is pre-incubated with the compound, the inhibition being irreversible and reversible for the copper and zinc compounds, respectively. The relative stability of such complexes was estimated by competitive equilibria with human serum albumin (HSA), monitored by CD spectroscopy. The copper species shows a log KCuL = 17.2, while the analogous zinc complex exhibits a log KZnL = 7.2. Molecular docking simulation studies show that the almost square planar geometry of the copper compound allows a direct coordination of the metal with two amino acids (Glu492, Asp563) of the enzyme at variance of the zinc compound which has a more tetrahedral geometry. Altogether, the data indicate that the different coordination geometry achieved by the two transition metal ions has an important role in modulating their efficiency as topoisomerase I inhibitors.
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Affiliation(s)
- Prafulla Katkar
- Dipartimento di Biologia, Università Tor Vergata di Roma, 00173 Roma, Italy.
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177
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Afzal O, Kumar S, Haider MR, Ali MR, Kumar R, Jaggi M, Bawa S. A review on anticancer potential of bioactive heterocycle quinoline. Eur J Med Chem 2014; 97:871-910. [PMID: 25073919 DOI: 10.1016/j.ejmech.2014.07.044] [Citation(s) in RCA: 532] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/08/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
Abstract
The advent of Camptothecin added a new dimension in the field anticancer drug development containing quinoline motif. Quinoline scaffold plays an important role in anticancer drug development as their derivatives have shown excellent results through different mechanism of action such as growth inhibitors by cell cycle arrest, apoptosis, inhibition of angiogenesis, disruption of cell migration, and modulation of nuclear receptor responsiveness. The anti-cancer potential of several of these derivatives have been demonstrated on various cancer cell lines. In this review we have compiled and discussed specifically the anticancer potential of quinoline derivatives, which could provide a low-height flying bird's eye view of the quinoline derived compounds to a medicinal chemist for a comprehensive and target oriented information for development of clinically viable anticancer drugs.
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Affiliation(s)
- Obaid Afzal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India
| | - Suresh Kumar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India
| | - Md Rafi Haider
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India
| | - Md Rahmat Ali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India
| | - Rajiv Kumar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India
| | - Manu Jaggi
- Dabur Research Foundation, Ghaziabad, Uttar Pradesh, India
| | - Sandhya Bawa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, New Delhi 110062, India.
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178
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D'Annessa I, Coletta A, Sutthibutpong T, Mitchell J, Chillemi G, Harris S, Desideri A. Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site. Nucleic Acids Res 2014; 42:9304-12. [PMID: 25056319 PMCID: PMC4132758 DOI: 10.1093/nar/gku654] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Human topoisomerase 1B has been simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to the enzyme bound to a simple linear DNA duplex. The presence of the more realistic supercoiled substrate facilitates the formation of larger number of protein–DNA interactions when compared to a simple linear duplex fragment. The number of protein–DNA hydrogen bonds doubles in proximity to the active site, affecting all of the residues in the catalytic pentad. The clamp over the DNA, characterized by the salt bridge between Lys369 and Glu497, undergoes reduced fluctuations when bound to the supercoiled minicircle. The linker domain of the enzyme, which is implicated in the controlled relaxation of superhelical stress, also displays an increased number of contacts with the minicircle compared to linear DNA. Finally, the more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA binding site involving four residues located on subdomain III. The simulation trajectories reveal significant changes in the interactions between the enzyme and the DNA for the more complex DNA topology, which are consistent with the experimental observation that the protein has a preference for binding to supercoiled DNA.
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Affiliation(s)
- Ilda D'Annessa
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Andrea Coletta
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | | | - Jonathan Mitchell
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | | | - Sarah Harris
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Alessandro Desideri
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
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179
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Aki-Yalcin E, Ertan-Bolelli T, Taskin-Tok T, Ozturk O, Ataei S, Ozen C, Yildiz I, Yalcin I. Evaluation of inhibitory effects of benzothiazole and 3-amino-benzothiazolium derivatives on DNA topoisomerase II by molecular modeling studies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:637-649. [PMID: 25027467 DOI: 10.1080/1062936x.2014.923039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
There has been considerable interest in DNA topoisomerases over the last decade, as they have been shown to be one of the major cellular targets in anticancer drug development. Previously we synthesized some benzothiazole derivatives and corresponding benzothiazolium forms, and tested their DNA inhibitory activity to develop novel antitumor agents. Among the 12 prepared compounds, compound BM3 (3-aminobenzothiazole-3-ium 4-methylbenzene sulfonate) exhibited extreme topoisomerase II inhibitory activity compared with the reference drug etoposide. We also tried to determine the DNA and enzyme binding abilities of BM3 and found that BM3 acted on topoisomerase II first at low doses, while it had also showed DNA minor groove binding properties at higher doses. In this study the interactions between DNA topoisomerase II and the compounds were examined in detail by molecular modelling studies such as molecular docking and pharmacophore analysis performed using Discovery Studio 3.5. As a result, it was found that benzothiazolium compounds exhibited a totally different mechanism than benzothiazoles by binding to the different amino acids at the active site of the protein molecule. 3-Aminobenzothiazoliums are worthy of carrying onto anticancer studies; BM3 especially would be a good anticancer candidate for preclinical studies.
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Affiliation(s)
- E Aki-Yalcin
- a Pharmaceutical Chemistry Department, Faculty of Pharmacy , Ankara University , Ankara , Turkey
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180
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Chu FM, Chang KT, Chen KM, Wei GT. Supercritical Fluid Extraction of Camptothecin from Nothapodytes Foetida. J CHIN CHEM SOC-TAIP 2014. [DOI: 10.1002/jccs.201300631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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181
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Zhao XB, Goto M, Song ZL, Morris-Natschke SL, Zhao Y, Wu D, Yang L, Li SG, Liu YQ, Zhu GX, Wu XB, Lee KH. Design and synthesis of new 7-(N-substituted-methyl)-camptothecin derivatives as potent cytotoxic agents. Bioorg Med Chem Lett 2014; 24:3850-3. [PMID: 25008456 DOI: 10.1016/j.bmcl.2014.06.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 11/30/2022]
Abstract
A series of novel 7-(N-substituted-methyl)-camptothecin derivatives was designed, synthesized, and evaluated for in vitro cytotoxicity against four human tumor cell lines, A-549, MDA-MB-231, KB, and KBvin. All of the derivatives showed promising in vitro cytotoxic activity against the tested tumor cell lines, with IC50 values ranging from 0.0023 to 1.11 μM, and were as or more potent than topotecan. Compounds 9d, 9e, and 9r exhibited the highest antiproliferative activity among all prepared derivatives. Furthermore, all of the compounds were more potent than paclitaxel against the multidrug-resistant (MDR) KBvin subline. With a concise efficient synthesis and potent cytotoxic profiles, especially significant activity towards KBvin, compounds 9d, 9e, and 9r merit further development as a new generation of camptothecin-derived anticancer clinical trial candidates.
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Affiliation(s)
- Xiao-Bo Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Masuo Goto
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Zi-Long Song
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Susan L Morris-Natschke
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Yu Zhao
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Dan Wu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Liu Yang
- Environmental and Municipal Engineering School, Lanzhou Jiaotong University, Lanzhou 730000, PR China
| | - Shu-Gang Li
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Ying-Qian Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China.
| | - Gao-Xiang Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Xiao-Bing Wu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, PR China
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, United States; Chinese Medicine Research and Development Center, China Medical University and Hospital, Taichung, Taiwan.
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182
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Anderson BG, Stivers JT. Variola type IB DNA topoisomerase: DNA binding and supercoil unwinding using engineered DNA minicircles. Biochemistry 2014; 53:4302-15. [PMID: 24945825 PMCID: PMC4089885 DOI: 10.1021/bi500571q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Type
IB topoisomerases unwind positive and negative DNA supercoils
and play a key role in removing supercoils that would otherwise accumulate
at replication and transcription forks. An interesting question is
whether topoisomerase activity is regulated by the topological state
of the DNA, thereby providing a mechanism for targeting the enzyme
to highly supercoiled DNA domains in genomes. The type IB enzyme from
variola virus (vTopo) has proven to be useful in addressing mechanistic
questions about topoisomerase function because it forms a reversible
3′-phosphotyrosyl adduct with the DNA backbone at a specific
target sequence (5′-CCCTT-3′) from which DNA unwinding
can proceed. We have synthesized supercoiled DNA minicircles (MCs)
containing a single vTopo target site that provides highly defined
substrates for exploring the effects of supercoil density on DNA binding,
strand cleavage and ligation, and unwinding. We observed no topological
dependence for binding of vTopo to these supercoiled MC DNAs, indicating
that affinity-based targeting to supercoiled DNA regions by vTopo
is unlikely. Similarly, the cleavage and religation rates of the MCs
were not topologically dependent, but topoisomers with low superhelical
densities were found to unwind more slowly than highly supercoiled
topoisomers, suggesting that reduced torque at low superhelical densities
leads to an increased number of cycles of cleavage and ligation before
a successful unwinding event. The K271E charge reversal mutant has
an impaired interaction with the rotating DNA segment that leads to
an increase in the number of supercoils that were unwound per cleavage
event. This result provides evidence that interactions of the enzyme
with the rotating DNA segment can restrict the number of supercoils
that are unwound. We infer that both superhelical density and transient
contacts between vTopo and the rotating DNA determine the efficiency
of supercoil unwinding. Such determinants are likely to be important
in regulating the steady-state superhelical density of DNA domains
in the cell.
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Affiliation(s)
- Breeana G Anderson
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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183
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Rolling circle amplification-based detection of human topoisomerase I activity on magnetic beads. Anal Biochem 2014; 451:42-4. [PMID: 24525043 DOI: 10.1016/j.ab.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/03/2014] [Accepted: 02/03/2014] [Indexed: 12/18/2022]
Abstract
A high-sensitivity assay has been developed for the detection of human topoisomerase I with single molecule resolution. The method uses magnetic sepharose beads to concentrate rolling circle products, produced by the amplification of DNA molecules circularized by topoisomerase I and detectable with a confocal microscope as single and discrete dots, once reacted with fluorescent probes. Each dot, corresponding to a single cleavage-religation event mediated by the enzyme, can be counted due to its high signal/noise ratio, allowing detection of 0.3pM enzyme and representing a valid method to detect the enzyme activity in highly diluted samples.
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184
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Akerman KJ, Fagenson AM, Cyril V, Taylor M, Muller MT, Akerman MP, Munro OQ. Gold(III) macrocycles: nucleotide-specific unconventional catalytic inhibitors of human topoisomerase I. J Am Chem Soc 2014; 136:5670-82. [PMID: 24694294 PMCID: PMC4004252 DOI: 10.1021/ja412350f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
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Topoisomerase
IB (Top1) is a key eukaryotic nuclear enzyme that
regulates the topology of DNA during replication and gene transcription.
Anticancer drugs that block Top1 are either well-characterized interfacial
poisons or lesser-known catalytic inhibitor compounds. Here we describe
a new class of cytotoxic redox-stable cationic Au3+ macrocycles
which, through hierarchical cluster analysis of cytotoxicity data
for the lead compound, 3, were identified as either poisons
or inhibitors of Top1. Two pivotal enzyme inhibition assays prove
that the compounds are true catalytic inhibitors of Top1. Inhibition
of human topoisomerase IIα (Top2α) by 3 was
2 orders of magnitude weaker than its inhibition of Top1, confirming
that 3 is a type I-specific catalytic inhibitor. Importantly,
Au3+ is essential for both DNA intercalation and enzyme
inhibition. Macromolecular simulations show that 3 intercalates
directly at the 5′-TA-3′ dinucleotide sequence targeted
by Top1 via crucial electrostatic interactions, which include π–π
stacking and an Au···O contact involving a thymine
carbonyl group, resolving the ambiguity of conventional (drug binds
protein) vs unconventional (drug binds substrate) catalytic inhibition
of the enzyme. Surface plasmon resonance studies confirm the molecular
mechanism of action elucidated by the simulations.
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Affiliation(s)
- Kate J Akerman
- School of Chemistry and Physics, University of KwaZulu-Natal , Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
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185
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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186
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Inoue Y, Ikegami Y, Sano K, Suzuki T, Yoshida H, Nakamura Y, Nakagawa H, Ishikawa T. Gefitinib enhances the antitumor activity of CPT-11 in vitro and in vivo by inhibiting ABCG2 but not ABCB1: a new clue to circumvent gastrointestinal toxicity risk. Chemotherapy 2014; 59:260-72. [PMID: 24457609 DOI: 10.1159/000357772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/05/2013] [Indexed: 01/12/2023]
Abstract
BACKGROUND Despite the potent antitumor activity of CPT-11, late-onset diarrhea owing to enterohepatic circulation of SN-38 is a critical issue. METHODS We aimed to evaluate the inhibitory potency of gefitinib against the ABCB1- or ABCG2-mediated excretion of CPT-11 and its active metabolite SN-38 in vitro and in vivo. RESULTS Gefitinib dose-dependently enhanced the antiproliferation activity of SN-38 in vitro by inhibiting ABCG2. The inhibitory effect of gefitinib on ABCB1 was marginal. When both CPT-11 and gefitinib were administered orally to nude mice bearing human lung cancer PC-6 cells, tumor growth was markedly suppressed. By gefitinib coadministration, the lactone forms of both CPT-11 and SN-38 in the tumor tissue increased more than 2-fold. CONCLUSIONS Gefitinib significantly enhances the antitumor efficacy of CPT-11 and its tumor distribution in vivo. Coadministration of gefitinib may provide a new means to reduce the dose of CPT-11 and to circumvent the gastrointestinal toxicity risk.
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Affiliation(s)
- Yutaka Inoue
- Department of Drug Metabolism and Disposition, Meiji Pharmaceutical University, Tokyo, Japan
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187
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Vlachakis D, Pavlopoulou A, Roubelakis MG, Feidakis C, Anagnou NP, Kossida S. 3D molecular modeling and evolutionary study of the Trypanosoma brucei DNA Topoisomerase IB, as a new emerging pharmacological target. Genomics 2014; 103:107-13. [DOI: 10.1016/j.ygeno.2013.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/19/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
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188
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The human topoisomerase 1B Arg634Ala mutation results in camptothecin resistance and loss of inter-domain motion correlation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2712-21. [DOI: 10.1016/j.bbapap.2013.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 11/22/2022]
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189
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Skorupka K, Han SK, Nam HJ, Kim S, Faham S. Protein design by fusion: implications for protein structure prediction and evolution. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2451-60. [PMID: 24311586 DOI: 10.1107/s0907444913022701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/12/2013] [Indexed: 01/21/2023]
Abstract
Domain fusion is a useful tool in protein design. Here, the structure of a fusion of the heterodimeric flagella-assembly proteins FliS and FliC is reported. Although the ability of the fusion protein to maintain the structure of the heterodimer may be apparent, threading-based structural predictions do not properly fuse the heterodimer. Additional examples of naturally occurring heterodimers that are homologous to full-length proteins were identified. These examples highlight that the designed protein was engineered by the same tools as used in the natural evolution of proteins and that heterodimeric structures contain a wealth of information, currently unused, that can improve structural predictions.
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Affiliation(s)
- Katarzyna Skorupka
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22093, USA
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190
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Kim H, Kang HJ, Lee JW, Park JD, Park KD, Shin HY, Ahn HS. Irinotecan, vincristine, cisplatin, cyclophosphamide, and etoposide for refractory or relapsed medulloblastoma/PNET in pediatric patients. Childs Nerv Syst 2013; 29:1851-8. [PMID: 23748464 DOI: 10.1007/s00381-013-2163-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE The treatment outcome of pediatric refractory or relapsed brain tumor is very dismal, and effective salvage chemotherapy is not established. The combination of irinotecan, vincristine, cisplatin, cyclophosphamide, and etoposide was administered to pediatric patients with refractory or relapsed brain tumors as a salvage treatment at our institution. METHODS The combination regimen was administered since June 2006 and consisted of irinotecan (300 mg/m(2), d0), vincristine (2 mg/m(2), d0), cisplatin (60 mg/m(2), d0), cyclophosphamide (1,000 mg/m(2), d1), and etoposide (100 mg/m(2)/day, d0-2). Patients could concurrently receive radiotherapy, surgery, and/or high-dose chemotherapy and stem cell rescue. The medical records of all patients were retrospectively analyzed. RESULTS Thirteen patients with refractory or relapsed brain tumor were included (medulloblastoma, n = 12; central nervous system primitive neuroectodermal tumor, n = 1). Median time from diagnosis to this combination chemotherapy was 30 months (range, 3-111 months), and median cycle administered was four cycles (range 1-22 cycles). Objective tumor response at the end of chemotherapy was 38.5 % including three patients with complete response and two with partial response. One patient showed complete response and achieved long-term survival with this combination chemotherapy, and two patients achieved long-term survival with multimodality treatments. There was no grade III or IV toxicity related to this combination chemotherapy except for thrombocytopenia and neutropenia. CONCLUSIONS The combination of irinotecan, vincristine, cisplatin, cyclophosphamide, and etoposide may produce objective responses in pediatric patients with refractory or relapsed medulloblastoma or primitive neuroectodermal tumor.
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Affiliation(s)
- Hyery Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
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191
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Lin Y, Beckham GT, Himmel ME, Crowley MF, Chu JW. Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures. J Phys Chem B 2013; 117:10750-8. [PMID: 23972069 DOI: 10.1021/jp405897q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yuchun Lin
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94704, United States
- State
Key Laboratory of Oral Diseases, West China
Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, People’s Republic of China
| | - Gregg T. Beckham
- Department
of Chemical Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | | | | | - Jhih-Wei Chu
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94704, United States
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192
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Siu FM, Pommier Y. Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study. Nucleic Acids Res 2013; 41:10010-9. [PMID: 24021629 PMCID: PMC3905861 DOI: 10.1093/nar/gkt791] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Topoisomerase IB (Top1) inhibitors, such as camptothecin (CPT), stabilize the Top1-DNA cleavage complex in a DNA sequence-dependent manner. The sequence selectivity of Top1 inhibitors is important for targeting specific genomic sequences of therapeutic value. However, the molecular mechanisms underlying this selectivity remain largely unknown. We performed molecular dynamics simulations to delineate structural, dynamic and energetic features that contribute to the differential sequence selectivity of the Top1 inhibitors. We found the sequence selectivity of CPT to be highly correlated with the drug binding energies, dynamic and structural properties of the linker domain. Chemical insights, gained by per-residue binding energy analysis revealed that the non-polar interaction between CPT and nucleotide at the +1 position of the cleavage site was the major (favorable) contributor to the total binding energy. Mechanistic insights gained by a potential of mean force analysis implicated that the drug dissociation step was associated with the sequence selectivity. Pharmaceutical insights gained by our molecular dynamics analyses explained why LMP-776, an indenoisoquinoline derivative under clinical development at the National Institutes of Health, displays different sequence selectivity when compared with camptothecin and its clinical derivatives.
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Affiliation(s)
- Fung-Ming Siu
- Center for High Performance Computing, Institute of Advanced Computing and Digital Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Boulevard, University Town of Shenzhen, Xili Nanshan, Shenzhen 518055, China, Department of Chemistry and Institutes of Molecular Technology for Drug Discovery and Synthesis, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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193
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Tesauro C, Morozzo della Rocca B, Ottaviani A, Coletta A, Zuccaro L, Arnò B, D'Annessa I, Fiorani P, Desideri A. Molecular mechanism of the camptothecin resistance of Glu710Gly topoisomerase IB mutant analyzed in vitro and in silico. Mol Cancer 2013; 12:100. [PMID: 24004603 PMCID: PMC3766703 DOI: 10.1186/1476-4598-12-100] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA topoisomerases are key enzymes that modulate the topological state of DNA through the breaking and rejoining of DNA strands. Human topoisomerase IB can be inhibited by several compounds that act through different mechanisms, including clinically used drugs, such as the derivatives of the natural compound camptothecin that reversibly bind the covalent topoisomerase-DNA complex, slowing down the religation of the cleaved DNA strand, thus inducing cell death. Three enzyme mutations, which confer resistance to irinotecan in an adenocarcinoma cell line, were recently identified but the molecular mechanism of resistance was unclear. METHODS The three resistant mutants have been investigated in S. cerevisiae model system following their viability in presence of increasing amounts of camptothecin. A systematical analysis of the different catalytic steps has been made for one of these mutants (Glu710Gly) and has been correlated with its structural-dynamical properties studied by classical molecular dynamics simulation. RESULTS The three mutants display a different degree of camptothecin resistance in a yeast cell viability assay. Characterization of the different steps of the catalytic cycle of the Glu710Gly mutant indicated that its resistance is related to a high religation rate that is hardly affected by the presence of the drug. Analysis of the dynamic properties through simulation indicate that the mutant displays a much lower degree of correlation in the motion between the different protein domains and that the linker almost completely loses its correlation with the C-terminal domain, containing the active site tyrosine. CONCLUSIONS These results indicate that a fully functional linker is required to confer camptothecin sensitivity to topoisomerase I since the destabilization of its structural-dynamical properties is correlated to an increase of religation rate and drug resistance.
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Affiliation(s)
- Cinzia Tesauro
- Department of Biology and Interuniversity Consortium, National Institute Biostructures and Biosystems (INBB), University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133 Italy.
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194
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Structural and functional interactions of the prostate cancer suppressor protein NKX3.1 with topoisomerase I. Biochem J 2013; 453:125-36. [PMID: 23557481 DOI: 10.1042/bj20130012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
NKX3.1 (NK3 homeobox 1) is a prostate tumour suppressor protein with a number of activities that are critical for its role in tumour suppression. NKX3.1 mediates the cellular response to DNA damage by interacting with ATM (ataxia telangiectasia mutated) and by activation of topoisomerase I. In the present study we characterized the interaction between NKX3.1 and topoisomerase I. The NKX3.1 homeodomain binds to a region of topoisomerase I spanning the junction between the core and linker domains. Loss of the topoisomerase I N-terminal domain, a region for frequent protein interactions, did not affect binding to NKX3.1 as was shown by the activation of Topo70 (N-terminal truncated topoisomerase I) in vitro. In contrast, NKX3.1 interacts with the enzyme reconstituted from peptide fragments of the core and linker active site domains, but inhibits the DNA-resolving activity of the reconstituted enzyme in vitro. The effect of NKX3.1 on both Topo70 and the reconstituted enzyme was seen in the presence and absence of camptothecin. Neither NKX3.1 nor CPT (camptothecin) had an effect on the interaction of the other with topoisomerase I. Therefore the interactions of NKX3.1 and CPT with the linker domain of topoisomerase I are mutually exclusive. However, in cells the effect of NKX3.1 on topoisomerase binding to DNA sensitized the cells to cellular toxicity and the induction of apoptosis by low doses of CPT. Lastly, topoisomerase I is important for the effect of NKX3.1 on cell survival after DNA damage as topoisomerase knockdown blocked the effect of NKX3.1 on clonogenicity after DNA damage. Therefore NKX3.1 and topoisomerase I interact in vitro and in cells to affect the CPT sensitivity and DNA-repair functions of NKX3.1.
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195
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Guschina TA, Soboleva SE, Nevinsky GA. Recognition of specific and nonspecific DNA by human lactoferrin. J Mol Recognit 2013; 26:136-48. [PMID: 23345104 DOI: 10.1002/jmr.2257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/08/2022]
Abstract
The general principles of recognition of nucleic acids by proteins are among the most exciting problems of molecular biology. Human lactoferrin (LF) is a remarkable protein possessing many independent biological functions, including interaction with DNA. In human milk, LF is a major DNase featuring two DNA-binding sites with different affinities for DNA. The mechanism of DNA recognition by LF was studied here for the first time. Electrophoretic mobility shift assay and fluorescence measurements were used to probe for interactions of the high-affinity DNA-binding site of LF with a series of model-specific and nonspecific DNA ligands, and the structural determinants of DNA recognition by LF were characterized quantitatively. The minimal ligands for this binding site were orthophosphate (K(i) = 5 mM), deoxyribose 5'-phosphate (K(i) = 3 mM), and different dNMPs (K(i) = 0.56-1.6 mM). LF interacted additionally with 9-12 nucleotides or nucleotide pairs of single- and double-stranded ribo- and deoxyribooligonucleotides of different lengths and sequences, mainly through weak additive contacts with internucleoside phosphate groups. Such nonspecific interactions of LF with noncognate single- and double-stranded d(pN)(10) provided ~6 to ~7.5 orders of magnitude of the enzyme affinity for any DNA. This corresponds to the Gibbs free energy of binding (ΔG(0)) of -8.5 to -10.0 kcal/mol. Formation of specific contacts between the LF and its cognate DNA results in an increase of the DNA affinity for the enzyme by approximately 1 order of magnitude (K(d) = 10 nM; ΔG(0) ≈ -11.1 kcal/mol). A general function for the LF affinity for nonspecific d(pN)(n) of different sequences and lengths was obtained, giving the K(d) values comparable with the experimentally measured ones. A thermodynamic model was constructed to describe the interactions of LF with DNA.
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Affiliation(s)
- Tat'yana A Guschina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
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196
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Wei NN, Hamza A, Hao C, Xiu Z, Zhan CG. Microscopic Modes and Free Energies for Topoisomerase I-DNA Covalent Complex Binding with Non-campothecin Inhibitors by Molecular Docking and Dynamics Simulations. Theor Chem Acc 2013; 132:10.1007/s00214-013-1379-z. [PMID: 24363608 PMCID: PMC3867144 DOI: 10.1007/s00214-013-1379-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Topoisomerase I (Topo1) has been identified as an attractive target for anticancer drug development due to its central role in facilitating the nuclear process of the DNA. It is essential for rational design of novel Topo1 inhibitors to reliably predict the binding structures of the Topo1 inhibitors interacting with the Topo1-DNA complex. The detailed binding structures and binding free energies for the Topo1-DNA complex interacting with typical non-camptothecin (CPT) Topo1 inhibitors have been examined by performing molecular docking, molecular dynamic (MD) simulations, and binding free energy calculations. The computational results provide valuable insights into the binding modes of the inhibitors binding with the Topo1-DNA complex and the key factors affecting the binding affinity. It has been demonstrated that the - stacking interaction with the DNA base pairs and the hydrogen bonding with Topo1 have the pivotal contributions to the binding structures and binding free energies, although the van der Waals and electrostatic interactions also significantly contribute to the stabilization of the binding structures. The calculated binding free energies are in good agreement with the available experiment activity data. The detailed binding modes and the crucial factors affecting the binding free energies obtained from the present computational studies may provide valuable insights for future rational design of novel, more potent Topo1 inhibitors.
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Affiliation(s)
- Ning-Ning Wei
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
- State Key Laboratory of Fine Chemicals, School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Adel Hamza
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Ce Hao
- State Key Laboratory of Fine Chemicals, School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Zhilong Xiu
- State Key Laboratory of Fine Chemicals, School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
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197
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Arakawa Y, Ozaki K, Okawa Y, Yamada H. Three missense mutations of DNA topoisomerase I in highly camptothecin-resistant colon cancer cell sublines. Oncol Rep 2013; 30:1053-8. [PMID: 23836376 PMCID: PMC3783056 DOI: 10.3892/or.2013.2594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/21/2013] [Indexed: 02/04/2023] Open
Abstract
Various anticancer drugs, including camptothecins and indolocarbazoles, target DNA topoisomerase I (Top1). We previously described the camptothecin-resistant colon cancer cell line DLDSNR6, which has a Gly365Ser missense mutation in Top1. In the present study, we established highly camptothecin-resistant sublines from DLDSNR6 cells by continuous exposure to higher camptothecin concentrations. The established sublines grew in the presence of 30 μM of camptothecin, but exhibited markedly retarded growth. In addition to Gly365Ser, these sublines harbored a Top1 Gly717Arg mutation and some had also a Top1 Gln421Arg mutation. Top1 activity was reduced to approximately one-eighth in highly resistant cell lines compared with that in parental DLD-1 cells. Resistant clones with 3 Top1 mutations including Gln421RArg exhibited the highest resistance to the indolocarbazole J-107088 in terms of the effect on the cell cycle distribution. The Gln421 mutation was equivalent to a mutation recently found in camptothecin biosynthesizing plants, but it has not previously been found in mammalian cells.
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Affiliation(s)
- Yasuhiro Arakawa
- Department of Oncology and Hematology, Jikei University School of Medicine, Minato‑Ku, Tokyo 105‑8471, Japan
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Arnò B, D’Annessa I, Tesauro C, Zuccaro L, Ottaviani A, Knudsen B, Fiorani P, Desideri A. Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant. PLoS One 2013; 8:e68404. [PMID: 23844196 PMCID: PMC3699648 DOI: 10.1371/journal.pone.0068404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/29/2013] [Indexed: 12/17/2022] Open
Abstract
A human/plasmodial hybrid enzyme, generated by swapping the human topoisomerase IB linker domain with the corresponding domain of the Plasmodium falciparum enzyme, has been produced and characterized. The hybrid enzyme displays a relaxation activity comparable to the human enzyme, but it is characterized by a much faster religation rate. The hybrid enzyme is also camptothecin resistant. A 3D structure of the hybrid enzyme has been built and its structural-dynamical properties have been analyzed by molecular dynamics simulation. The analysis indicates that the swapped plasmodial linker samples a conformational space much larger than the corresponding domain in the human enzyme. The large linker conformational variability is then linked to important functional properties such as an increased religation rate and a low drug reactivity, demonstrating that the linker domain has a crucial role in the modulation of the topoisomerase IB activity.
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Affiliation(s)
- Barbara Arnò
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Ilda D’Annessa
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Cinzia Tesauro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Laura Zuccaro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Birgitta Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Alessandro Desideri
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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Dogra S, Awasthi P, Tripathi S, Pradeep T, Nair MS, Barthwal R. NMR-based structure of anticancer drug mitoxantrone stacked with terminal base pair of DNA hexamer sequence d-(ATCGAT)2. J Biomol Struct Dyn 2013; 32:1164-83. [DOI: 10.1080/07391102.2013.809021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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200
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Ucuncuoglu N, Andricioaei I, Sari L. Insights from simulations into the mechanism of human topoisomerase I: Explanation for a seeming controversy in experiments. J Mol Graph Model 2013; 44:286-96. [DOI: 10.1016/j.jmgm.2013.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 11/27/2022]
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