1
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Targeting mitochondria as a potential therapeutic strategy against chemoresistance in cancer. Biomed Pharmacother 2023; 160:114398. [PMID: 36773523 DOI: 10.1016/j.biopha.2023.114398] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/21/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
The importance of mitochondria is not only limited to energy generation but also in several physical and chemical processes critical for cell survival. Mitochondria play an essential role in cellular apoptosis, calcium ion transport and cellular metabolism. Mutation in the nuclear and mitochondrial genes, altered oncogenes/tumor suppressor genes, and deregulated signalling for cell viability are major reasons for cancer progression and chemoresistance. The development of drug resistance in cancer patients is a major challenge in cancer treatment as the resistant cells are often more aggressive. The drug resistant cells of numerous cancer types exhibit the deregulation of mitochondrial function. The increased biogenesis of mitochondria and its dynamic alteration contribute to developing resistance. Further, a small subpopulation of cancer stem cells in the heterogeneous tumor is primarily responsible for chemoresistance and has an attribute of mitochondrial dysfunction. This review highlights the critical role of mitochondrial dysfunction in chemoresistance in cancer cells through the processes of apoptosis, autophagy/mitophagy, and cancer stemness. Mitochondria-targeted therapeutic strategies might help reduce cancer progression and chemoresistance induced by various cancer drugs.
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2
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Mechanism of action of non-camptothecin inhibitor Genz-644282 in topoisomerase I inhibition. Commun Biol 2022; 5:982. [PMID: 36114357 PMCID: PMC9481636 DOI: 10.1038/s42003-022-03920-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractTopoisomerase I (TOP1) controls the topological state of DNA during DNA replication, and its dysfunction due to treatment with an inhibitor, such as camptothecin (CPT), causes replication arrest and cell death. Although CPT has excellent cytotoxicity, it has the disadvantage of instability under physiological conditions. Therefore, new types of TOP1 inhibitor have attracted particular attention. Here, we characterised the effect of a non-camptothecin inhibitor, Genz-644282 (Genz). First, we found that treatment with Genz showed cytotoxicity by introducing double-strand breaks (DSBs), which was suppressed by co-treatment with aphidicolin. Genz-induced DSB formation required the functions of TOP1. Next, we explored the advantages of Genz over CPT and found it was effective against CPT-resistant TOP1 carrying either N722S or N722A mutation. The effect of Genz was also confirmed at the cellular level using a CPT-resistant cell line carrying N722S mutation in the TOP1 gene. Moreover, we found arginine residue 364 plays a crucial role for the binding of Genz. Because tyrosine residue 723 is the active centre for DNA cleavage and re-ligation by TOP1, asparagine residue 722 plays crucial roles in the accessibility of the drug. Here, we discuss the mechanism of action of Genz on TOP1 inhibition.
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3
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da Silva MM, Ribeiro GH, de Camargo MS, Ferreira AG, Ribeiro L, Barbosa MIF, Deflon VM, Castelli S, Desideri A, Corrêa RS, Ribeiro AB, Nicolella HD, Ozelin SD, Tavares DC, Batista AA. Ruthenium(II) Diphosphine Complexes with Mercapto Ligands That Inhibit Topoisomerase IB and Suppress Tumor Growth In Vivo. Inorg Chem 2021; 60:14174-14189. [PMID: 34477373 DOI: 10.1021/acs.inorgchem.1c01539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ruthenium(II) complexes (Ru1-Ru5), with the general formula [Ru(N-S)(dppe)2]PF6, bearing two 1,2-bis(diphenylphosphino)ethane (dppe) ligands and a series of mercapto ligands (N-S), have been developed. The combination of these ligands in the complexes endowed hydrophobic species with high cytotoxic activity against five cancer cell lines. For the A549 (lung) and MDA-MB-231 (breast) cancer cell lines, the IC50 values of the complexes were 288- to 14-fold lower when compared to cisplatin. Furthermore, the complexes were selective for the A549 and MDA-MB-231 cancer cell lines compared to the MRC-5 nontumor cell line. The multitarget character of the complexes was investigated by using calf thymus DNA (CT DNA), human serum albumin, and human topoisomerase IB (hTopIB). The complexes potently inhibited hTopIB. In particular, complex [Ru(dmp)(dppe)2]PF6 (Ru3), bearing the 4,6-diamino-2-mercaptopyrimidine (dmp) ligand, effectively inhibited hTopIB by acting on both the cleavage and religation steps of the catalytic cycle of this enzyme. Molecular docking showed that the Ru1-Ru5 complexes have binding affinity by active sites on the hTopI and hTopI-DNA, mainly via π-alkyl and alkyl hydrophobic interactions, as well as through hydrogen bonds. Complex Ru3 displayed significant antitumor activity against murine melanoma in mouse xenograph models, but this complex did not damage DNA, as revealed by Ames and micronucleus tests.
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Affiliation(s)
- Monize M da Silva
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Gabriel H Ribeiro
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Mariana S de Camargo
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Antônio G Ferreira
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Leandro Ribeiro
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Marília I F Barbosa
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Victor M Deflon
- Instituto de Química de São Carlos, Universidade de São Paulo, CEP 13565-905 São Carlos, São Paulo, Brazil
| | - Silvia Castelli
- Dipartimento di Biologia, Università Tor Vergata di Roma, 00133 Rome, Italy
| | | | - Rodrigo S Corrêa
- Departamento de Química, Universidade Federal de Ouro Preto, CEP 35400-000 Ouro Preto, Minas Gerais, Brazil
| | - Arthur B Ribeiro
- Universidade de Franca, CEP 14404-600, Franca, São Paulo, Brazil
| | | | - Saulo D Ozelin
- Universidade de Franca, CEP 14404-600, Franca, São Paulo, Brazil
| | - Denise C Tavares
- Universidade de Franca, CEP 14404-600, Franca, São Paulo, Brazil
| | - Alzir A Batista
- Departamento de Química, Universidade Federal de São Carlos, CP 676, CEP 13565-905 São Carlos, São Paulo, Brazil
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4
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Soren BC, Babu Dasari J, Ottaviani A, Messina B, Andreotti G, Romeo A, Iacovelli F, Falconi M, Desideri A, Fiorani P. In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB. Int J Mol Sci 2021; 22:7455. [PMID: 34299074 PMCID: PMC8306514 DOI: 10.3390/ijms22147455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Giada Andreotti
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alice Romeo
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
- Institute of Translational Pharmacology, National Research Council, CNR, Via del Fosso del Cavaliere 100, 00133 Rome, Italy
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5
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Ottaviani A, Iacovelli F, Fiorani P, Desideri A. Natural Compounds as Therapeutic Agents: The Case of Human Topoisomerase IB. Int J Mol Sci 2021; 22:4138. [PMID: 33923641 PMCID: PMC8073192 DOI: 10.3390/ijms22084138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
Natural products are widely used as source for drugs development. An interesting example is represented by natural drugs developed against human topoisomerase IB, a ubiquitous enzyme involved in many cellular processes where several topological problems occur due the formation of supercoiled DNA. Human topoisomerase IB, involved in the solution of such problems relaxing the DNA cleaving and religating a single DNA strand, represents an important target in anticancer therapy. Several natural compounds inhibiting or poisoning this enzyme are under investigation as possible new drugs. This review summarizes the natural products that target human topoisomerase IB that may be used as the lead compounds to develop new anticancer drugs. Moreover, the natural compounds and their derivatives that are in clinical trial are also commented on.
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Affiliation(s)
- Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
- 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, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
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6
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Soren BC, Dasari JB, Ottaviani A, Iacovelli F, Fiorani P. Topoisomerase IB: a relaxing enzyme for stressed DNA. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:18-25. [PMID: 35582040 PMCID: PMC9094055 DOI: 10.20517/cdr.2019.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 11/12/2022]
Abstract
DNA topoisomerase I enzymes relieve the torsional strain in DNA; they are essential for fundamental molecular processes such as DNA replication, transcription, recombination, and chromosome condensation; and act by cleaving and then religating DNA strands. Over the past few decades, scientists have focused on the DNA topoisomerases biological functions and established a unique role of Type I DNA topoisomerases in regulating gene expression and DNA chromosome condensation. Moreover, the human enzyme is being investigated as a target for cancer chemotherapy. The active site tyrosine is responsible for initiating two transesterification reactions to cleave and then religate the DNA backbone, allowing the release of superhelical tension. The different steps of the catalytic mechanism are affected by various inhibitors; some of them prevent the interaction between the enzyme and the DNA while others act as poisons, leading to TopI-DNA lesions, breakage of DNA, and eventually cellular death. In this review, our goal is to provide an overview of mechanism of human topoisomerase IB action together with the different types of inhibitors and their effect on the enzyme functionality.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Present address: Department of Research and Application Development, Biogenex Life Sciences, Telangana 501510, India
| | - Alessio Ottaviani
- Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy.,Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
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7
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Wang Z, D'Annessa I, Tesauro C, Ottaviani A, Soren BC, Dasari JB, Messina B, Thareparambil A, Fiorani P. The human DNA topoisomerase I mutant Gly717Asp: Higher religation rate is not always associated with camptothecin resistance. Arch Biochem Biophys 2019; 663:165-172. [PMID: 30653963 DOI: 10.1016/j.abb.2019.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 11/15/2022]
Abstract
DNA topoisomerases are key enzyme responsible for modulating the topological state of the DNA by breaking and rejoining of DNA strand. Characterization of a Gly717Asp mutation in the human topoisomerase was performed using several catalytic assays. The mutant enzyme was shown to have comparable cleavage and fast religation rate as compared to the wild-type protein. Addition of the anticancer drug camptothecin significantly reduced the religation step. The simulative approaches and analysis of the cleavage/religation equilibrium indicate that the mutation is able to modify the architecture of the drug binding site, increasing the persistence of the drug for the enzyme-DNA covalent complex. Taken together these results indicate that the structure modification of the drug binding site is the key reason for the increasing CPT persistence and furthermore provide the possibility for new anti-cancer drug discovery.
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Affiliation(s)
- Zhenxing Wang
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ilda D'Annessa
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Cinzia Tesauro
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Anil Thareparambil
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica 1, 00133, Rome, Italy; Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome, 00133, Italy.
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8
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Wang Z, Ouyang H, Tesauro C, Ottaviani A, He Y, Fiorani P, Xie H, Desideri A, Fu Z. Real-time analysis of cleavage and religation activity of human topoisomerase 1 based on ternary fluorescence resonance energy transfer DNA substrate. Arch Biochem Biophys 2018; 643:1-6. [PMID: 29458004 DOI: 10.1016/j.abb.2018.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 12/22/2022]
Abstract
Human topoisomerase 1B is a ubiquitous and essential enzyme involved in relaxing the topological state of supercoiled DNA to allow the progression of fundamental DNA metabolism. Its enzymatic catalytic cycle consists of cleavage and religation reaction. A ternary fluorescence resonance energy transfer biosensor based on a suicide DNA substrate conjugated with three fluorophores has been developed to monitor both cleavage and religation Topoisomerase I catalytic function. The presence of fluorophores does not alter the specificity of the enzyme catalysis on the DNA substrate. The enzyme-mediated reaction can be tracked in real-time by simple fluorescence measurement, avoiding the use of risky radioactive substrate labeling and time-consuming denaturing gel electrophoresis. The method is applied to monitor the perturbation brought by single mutation on the cleavage or religation reaction and to screen the effect of the camptothecin anticancer drug monitoring the energy transfer decrease during religation reaction. Pathological mutations usually affect only the cleavage or the religation reaction and the proposed approach represent a fast protocol for assessing chemotherapeutic drug efficacy and analyzing mutant's properties.
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Affiliation(s)
- Zhenxing Wang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China; Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hui Ouyang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Cinzia Tesauro
- 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
| | - Yong He
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, Rome 00133, Italy
| | - Hui Xie
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy.
| | - Zhifeng Fu
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Ministry of Education), College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China.
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Zhang H, Seol Y, Agama K, Neuman KC, Pommier Y. Distribution bias and biochemical characterization of TOP1MT single nucleotide variants. Sci Rep 2017; 7:8614. [PMID: 28819183 PMCID: PMC5561071 DOI: 10.1038/s41598-017-09258-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial topoisomerase I (TOP1MT) is a type IB topoisomerase encoded in the nucleus of vertebrate cells. In contrast to the other five human topoisomerases, TOP1MT possesses two high frequency single nucleotide variants (SNVs), rs11544484 (V256I, Minor Allele Frequency = 0.27) and rs2293925 (R525W, MAF = 0.45), which tend to be mutually exclusive across different human ethnic groups and even more clearly in a cohort of 129 US patients with breast cancer and in the NCI-60 cancer cell lines. We expressed these two TOP1MT variants and the double-variant (V256I-R525W) as recombinant proteins, as well as a less common variant E168G (rs200673353, MAF = 0.001), and studied their biochemical properties by magnetic tweezers-based supercoil relaxation and classical DNA relaxation assays. Variants showed reduced DNA relaxation activities, especially the V256I variant towards positively supercoiled DNA. We also found that the V256I variant was enriched to MAF = 0.64 in NCI-60 lung carcinoma cell lines, whereas the TOP1MT R525W was enriched to MAF = 0.65 in the NCI-60 melanoma cell lines. Moreover, TOP1MT expression correlated with the 256 variants in the NCI-60 lung carcinoma cell lines, valine with high expression and isoleucine with low expression. Our results are discussed in the context of evolution between the nuclear and mitochondrial topoisomerases and potential cancer predisposition.
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Affiliation(s)
- Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD, 20892, USA.
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10
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Andersen MB, Tesauro C, Gonzalez M, Kristoffersen EL, Alonso C, Rubiales G, Coletta A, Frøhlich R, Stougaard M, Ho YP, Palacios F, Knudsen BR. Advantages of an optical nanosensor system for the mechanistic analysis of a novel topoisomerase I targeting drug: a case study. NANOSCALE 2017; 9:1886-1895. [PMID: 28094391 DOI: 10.1039/c6nr06848k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The continuous need for the development of new small molecule anti-cancer drugs calls for easily accessible sensor systems for measuring the effect of vast numbers of new drugs on their potential cellular targets. Here we demonstrate the use of an optical DNA biosensor to unravel the inhibitory mechanism of a member of a new family of small molecule human topoisomerase I inhibitors, the so-called indeno-1,5-naphthyridines. By analysing human topoisomerase I catalysis on the biosensor in the absence or presence of added drug complemented with a few traditional assays, we demonstrate that the investigated member of the indeno-1,5-naphthyridine family inhibited human topoisomerase I activity by blocking enzyme-DNA dissociation. To our knowledge, this represents the first characterized example of a small molecule drug that inhibits a post-ligation step of catalysis. The elucidation of a completely new and rather surprising drug mechanism-of-action using an optical real time sensor highlights the value of this assay system in the search for new topoisomerase I targeting small molecule drugs.
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Affiliation(s)
- Marie B Andersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - María Gonzalez
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Emil L Kristoffersen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Concepción Alonso
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Gloria Rubiales
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Andrea Coletta
- Department of Chemistry, Langelandsgade 140, Aarhus University, 8000 Aarhus C, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
| | - Magnus Stougaard
- Department of Pathology, Nørrebrogade 44 building 18B, Aarhus University, Denmark
| | - Yi-Ping Ho
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark. and Interdisciplinary Nanoscience Center, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark and Division of Biomedical Engineering, Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia and Centro de Investigación Lascaray (Lascaray Research Center), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain
| | - Birgitta R Knudsen
- Department of Molecular Biology and Genetics, C. F. Møllers Allé 3, Bldg 1131, Aarhus University, 8000 Aarhus C, Denmark.
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11
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Advances in the Chemistry of Natural and Semisynthetic Topoisomerase I/II Inhibitors. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2017. [DOI: 10.1016/b978-0-444-63929-5.00002-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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12
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Chandramouli B, Chillemi G. Conformational Dynamics of Lysine Methyltransferase Smyd2. Insights into the Different Substrate Crevice Characteristics of Smyd2 and Smyd3. J Chem Inf Model 2016; 56:2467-2475. [PMID: 27959541 DOI: 10.1021/acs.jcim.6b00652] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Smyd2, the SET and MYND domain containing protein lysine methyltransferase, targets histone and nonhistone substrates. Methylation of nonhistone substrates has direct implications in cancer development and progression. Dynamic regulation of Smyd2 activity and the structural basis of broad substrate specificity still remain elusive. Herein, we report on extensive molecular dynamics simulations on a full length Smyd2 in the presence and absence of AdoMet cofactor (covering together 1.3 μs of sampling), and the accompanying conformational transitions. Additionally, dynamics of the C-terminal domain (CTD) and structural features of substrate crevices of Smyd2 and Smyd3 are compared. The CTD of Smyd2 exhibits conformational flexibility in both states. In the holo form, however, it undergoes larger hinge motions resulting in more opened configurations than the apo form, which is confined around the partially open starting X-ray configuration. AdoMet binding triggers increased elasticity of the CTD leading Smyd2 to adopt fully opened configurations, which completely exposes the substrate binding crevice. These long-range concerted motions highlight Smyd2's ability to target substrates of varying sizes. Substrate crevices of Smyd2 and Smyd3 show distinct features in terms of spatial, hydration, and electrostatic properties that emphasize their characteristic modes of substrates interaction and entry pathways for inhibitor binding. On the whole, our study shows how the elasticity and hinge motion of the CTD regulate its functional role and underpin the basis of broad substrate specificity of Smyd2. We also highlight the specific structural principles that guide substrate and inhibitor binding to Smyd2 and Smyd3.
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Affiliation(s)
| | - Giovanni Chillemi
- SCAI-SuperComputing Applications and Innovation Department, CINECA ,Via dei Tizii 6, 00185 Rome, Italy
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13
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Girstun A, Ishikawa T, Kowalska-Loth B, Czubaty A, Staron K. Subnuclear Localization of Human Topoisomerase I. J Cell Biochem 2016; 118:407-419. [DOI: 10.1002/jcb.25654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Agnieszka Girstun
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Takao Ishikawa
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Barbara Kowalska-Loth
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Alicja Czubaty
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
| | - Krzysztof Staron
- Department of Molecular Biology; Institute of Biochemistry; Faculty of Biology; University of Warsaw; Warsaw Poland
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14
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Jensen NF, Agama K, Roy A, Smith DH, Pfister TD, Rømer MU, Zhang HL, Doroshow JH, Knudsen BR, Stenvang J, Brünner N, Pommier Y. Characterization of DNA topoisomerase I in three SN-38 resistant human colon cancer cell lines reveals a new pair of resistance-associated mutations. J Exp Clin Cancer Res 2016; 35:56. [PMID: 27029323 PMCID: PMC4815242 DOI: 10.1186/s13046-016-0335-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/23/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND DNA topoisomerase I (Top1) is a DNA unwinding protein and the specific target of the camptothecin class of chemotherapeutic drugs. One of these, irinotecan, acting through its active metabolite SN-38, is used in the treatment of metastatic colorectal cancer. However, resistance to irinotecan represents a major clinical problem. Since molecular alterations in Top1 may result in resistance to irinotecan, we characterized Top1 in three human colon cancer cell lines with acquired resistance to SN-38. METHODS Three SN-38 resistant (20-67 fold increased resistance) cell lines were generated and compared to wild-type parental cells with regards to: TOP1 gene copy number and gene sequence, Top1 expression (mRNA and protein), Top1 enzymatic activity in the absence and presence of drug, and Top1-DNA cleavage complexes in drug treated cells. TOP1 mutations were validated by PCR using mutant specific primers. Furthermore, cross-resistance to two indenoisoquinoline Top1-targeting drugs (NSC 725776 and NSC 743400) and two Top2-targeting drugs (epirubicin and etoposide) was investigated. RESULTS Two of three SN-38 resistant cell lines carried TOP1 gene copy number aberrations: A TOP1 gene copy gain and a loss of chromosome 20, respectively. One resistant cell line harbored a pair of yet unreported TOP1 mutations (R364K and G717R) in close proximity to the drug binding site. Mutant TOP1 was expressed at a markedly higher level than wild-type TOP1. None or very small reductions were observed in Top1 expression or Top1 activity in the absence of drug. In all three SN-38 resistant cell lines Top1 activity was maintained in the presence of high concentrations of SN-38. None or only partial cross-resistance were observed for etoposide and epirubicin, respectively. SN-38 resistant cells with wild-type TOP1 remained sensitive to NSC 743400, while cells with mutant TOP1 was fully cross-resistant to both indenoisoquinolines. Top1-DNA cleavage complex formation following drug treatment supported the other findings. CONCLUSIONS This study adds to the growing knowledge about resistance mechanisms for Top1-targeting chemotherapeutic drugs. Importantly, two yet unreported TOP1 mutations were identified, and it was underlined that cross-resistance to the new indenoisoquinoline drugs depends on the specific underlying molecular mechanism of resistance to SN-38.
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Affiliation(s)
- Niels Frank Jensen
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Keli Agama
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
| | - Amit Roy
- />Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
- />Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali 844102 India
| | - David Hersi Smith
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- />Dako Denmark A/S, R&D, Produktionsvej 42, DK-2600 Glostrup, Denmark
| | - Thomas D. Pfister
- />Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Maria Unni Rømer
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- />Department for Clinical Physiology and Nuclear Medicine, Frederiksberg Hospital, Nordre Fasanvej 57, DK-2000 Frederiksberg C, Denmark
| | - Hong-Liang Zhang
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
| | - James H. Doroshow
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
- />Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702 USA
| | - Birgitta R. Knudsen
- />Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, DK-8000 Aarhus C, Denmark
| | - Jan Stenvang
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Nils Brünner
- />Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Section for Molecular Disease Biology, University of Copenhagen, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yves Pommier
- />National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Molecular Pharmacology, 37 Convent Drive, Building 37, Room 5068, Bethesda, MD 20892-4255 USA
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15
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Rushworth D, Alpert A, Santana-Carrero R, Olivares S, Spencer D, Cooper LJN. Antithymidylate resistance enables transgene selection and cell survival for T cells in the presence of 5-fluorouracil and antifolates. Gene Ther 2015; 23:119-28. [PMID: 26273805 DOI: 10.1038/gt.2015.88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/11/2015] [Accepted: 08/05/2015] [Indexed: 12/31/2022]
Abstract
Antithymidylates (AThy) constitute a class of drugs used in the treatment of cancers such as lung, colon, breast and pancreas. These drugs inhibit DNA synthesis by targeting the enzymes dihydrofolate reductase (DHFR) and/or thymidylate synthase (TYMS). AThys effectively inhibit cancer cells, and also inhibit T cells, preventing anticancer immunity, which might otherwise develop from AThy-induced cancer destruction. We establish that T cells expressing mutant DHFR--DHFR L22F, F31S (DHFR(FS))--and/or mutant TYMS--TYMS T51S, G52S (TYMS(SS))-effectively survive in toxic concentrations of AThys methotrexate, pemetrexed and 5-fluorouracil. Furthermore, we show that DHFR(FS) permitted rapid selection of an inducible suicide transgene in T cells. These findings demonstrate that AThy resistances prevent AThy cytotoxicity to T cells while permitting selection of important transgenes. This technological development could enhance in vitro and in vivo survival and selection of T-cell therapeutics being designed for a broad range of cancers.
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Affiliation(s)
- D Rushworth
- Division of Pediatrics, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Unit 907, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - A Alpert
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - R Santana-Carrero
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA.,University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States Minor Outlying Islands
| | - S Olivares
- Division of Pediatrics, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Unit 907, Houston, TX, USA
| | - D Spencer
- Bellicum Pharmaceuticals, Houston, TX, USA
| | - L J N Cooper
- Division of Pediatrics, Children's Cancer Hospital, The University of Texas MD Anderson Cancer Center, Unit 907, Houston, TX, USA.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
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16
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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: 1.2] [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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17
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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: 1.1] [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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Roy K, Chanfreau G. Stress-induced nuclear RNA degradation pathways regulate yeast bromodomain factor 2 to promote cell survival. PLoS Genet 2014; 10:e1004661. [PMID: 25232960 PMCID: PMC4169253 DOI: 10.1371/journal.pgen.1004661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/11/2014] [Indexed: 11/23/2022] Open
Abstract
Bromodomain proteins are key regulators of gene expression. How the levels of these factors are regulated in specific environmental conditions is unknown. Previous work has established that expression of yeast Bromodomain factor 2 (BDF2) is limited by spliceosome-mediated decay (SMD). Here we show that BDF2 is subject to an additional layer of post-transcriptional control through RNase III-mediated decay (RMD). We found that the yeast RNase III Rnt1p cleaves a stem-loop structure within the BDF2 mRNA to down-regulate its expression. However, these two nuclear RNA degradation pathways play distinct roles in the regulation of BDF2 expression, as we show that the RMD and SMD pathways of the BDF2 mRNA are differentially activated or repressed in specific environmental conditions. RMD is hyper-activated by salt stress and repressed by hydroxyurea-induced DNA damage while SMD is inactivated by salt stress and predominates during DNA damage. Mutations of cis-acting signals that control SMD and RMD rescue numerous growth defects of cells lacking Bdf1p, and show that SMD plays an important role in the DNA damage response. These results demonstrate that specific environmental conditions modulate nuclear RNA degradation pathways to control BDF2 expression and Bdf2p-mediated gene regulation. Moreover, these results show that precise dosage of Bromodomain factors is essential for cell survival in specific environmental conditions, emphasizing their importance for controlling chromatin structure and gene expression in response to environmental stress. Cells adapt to changes in the environment through modulating gene expression at both the RNA and protein levels. RNA degradation plays a central role in this adaption response, by controlling the stability of specific mRNAs to optimize protein production in different conditions. In this study, we show that the gene encoding Bromodomain Factor 2 (BDF2) is tightly regulated according to environmental conditions by two distinct RNA degradation mechanisms. We show that these RNA degradation pathways are critical for cell growth in specific conditions. Our study suggests that environmental modulation of nuclear RNA degradation pathways is a previously unappreciated aspect of gene expression control.
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Affiliation(s)
- Kevin Roy
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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19
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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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Silvestris N, Simone G, Partipilo G, Scarpi E, Lorusso V, Brunetti AE, Maiello E, Paradiso A, Mangia A. CES2, ABCG2, TS and Topo-I primary and synchronous metastasis expression and clinical outcome in metastatic colorectal cancer patients treated with first-line FOLFIRI regimen. Int J Mol Sci 2014; 15:15767-77. [PMID: 25198900 PMCID: PMC4200864 DOI: 10.3390/ijms150915767] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/22/2014] [Accepted: 09/02/2014] [Indexed: 01/31/2023] Open
Abstract
Enzymatic activation of irinotecan (CPT-11) is due to carboxylesterase (CES), and its pharmacological behavior is influenced by drug resistance-related proteins. We previously reported that the clinical response and prognosis of metastatic colorectal cancer (mCRC) patients did not differ in tumors with different thymidylate synthase (TS) or topoisomerase-I (Topo-I) expression. Using immunohistochemistry (IHC), we evaluated the biological role of CES2 and the expression of breast cancer resistance protein (BCRP/ABCG2) in 58 consecutive mCRC patients, who had undergone a first-line CPT-11/5-FU/leucovirin (FOLFIRI) regimen. The expression of these proteins was also examined in a group of synchronous lymph nodes and liver metastases. Furthermore, all samples were revaluated for TS and Topo-I expression. High expression of CES2, ABCG2, TS and Topo-I was observed in 55%, 56%, 38% and 49% of patients, respectively. There was a significant association between high TS and high ABCG2 expression (p = 0.049). Univariate analysis showed that only TS expression significantly impacted on time to progression (p = 0.005). Moreover, Cox’ multivariate analysis revealed that TS expression was significantly associated with overall survival (p = 0.01). No significant correlation was found between investigated markers expression and clinical response. Topo-I expression resulted in being significantly higher in liver metastases with respect to the corresponding primary tumors (p < 0.0001), emphasizing the role of Topo-I expression in metastatic cancer biology. In primary tumor tissues, CES2 expression tended to be higher than that observed in liver metastasis tissues (p = 0.05). These preliminary data may suggest CES2 over-expression as a potential marker of malignant phenotype. In light of these findings, we suggest that Topo-I expression together with TS expression could be associated with metastatic progression of CRC. Further studies are warranted with the aim of evaluating the potential predictive and prognostic role of CES2 and ABCG2 in larger series of patients.
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Affiliation(s)
- Nicola Silvestris
- Medical Oncology Unit, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Giovanni Simone
- Pathology Department, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Giulia Partipilo
- Functional Biomorphology Laboratory, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Emanuela Scarpi
- IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (I.R.S.T.), 47014 Meldola, Italy.
| | - Vito Lorusso
- Medical Oncology Unit, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Anna Elisabetta Brunetti
- Medical Oncology Unit, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Evaristo Maiello
- Oncology Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Viale Cappuccini 1, 71013 San Giovanni Rotondo, Italy.
| | - Angelo Paradiso
- Experimental Medical Oncology, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
| | - Anita Mangia
- Functional Biomorphology Laboratory, National Cancer Research Centre-Istituto Tumori "Giovanni Paolo II", Viale Orazio Flacco 65, 70124 Bari, Italy.
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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: 2.4] [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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22
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Roy A, Tesauro C, Frøhlich R, Hede MS, Nielsen MJ, Kjeldsen E, Bonven B, Stougaard M, Gromova I, Knudsen BR. Decreased camptothecin sensitivity of the stem-cell-like fraction of Caco2 cells correlates with an altered phosphorylation pattern of topoisomerase I. PLoS One 2014; 9:e99628. [PMID: 24960044 PMCID: PMC4069021 DOI: 10.1371/journal.pone.0099628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 05/17/2014] [Indexed: 12/27/2022] Open
Abstract
The CD44+ and CD44− subpopulations of the colorectal cancer cell line Caco2 were analyzed separately for their sensitivities to the antitumor drug camptothecin. CD44+ cells were less sensitive to camptothecin than CD44− cells. The relative resistance of CD44+ cells was correlated with (i) reduced activity of the nuclear enzyme topoisomerase I and (ii) insensitivity of this enzyme to camptothecin when analyzed in extracts. In contrast, topoisomerase I activity was higher in extracts from CD44− cells and the enzyme was camptothecin sensitive. Topoisomerase I from the two subpopulations were differentially phosphorylated in a manner that appeared to determine the drug sensitivity and activity of the enzyme. This finding was further supported by the fact that phosphorylation of topoisomerase I in CD44+ cell extract by protein kinase CK2 converted the enzyme to a camptothecin sensitive, more active form mimicking topoisomerase I in extracts from CD44− cells. Conversely, dephosphorylation of topoisomerase I in extracts from CD44− cells rendered the enzyme less active and camptothecin resistant. These findings add to our understanding of chemotherapy resistance in the Caco2 CD44+ cancer stem cell model.
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Affiliation(s)
- Amit Roy
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Cinzia Tesauro
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Rikke Frøhlich
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria J. Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eigil Kjeldsen
- Hemodiagnostic Laboratory, Cancercytogenetic Section, Aarhus University Hospital, Aarhus, Denmark
| | - Bjarne Bonven
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Magnus Stougaard
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Irina Gromova
- Genome Integrity Unit, Proteomics in Cancer, Danish Cancer Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- * E-mail:
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23
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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: 0.6] [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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24
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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: 1.2] [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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