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Simultaneous mass spectrometry analysis of cisplatin with oligonucleotide-peptide mixtures: implications for the mechanism of action. J Biol Inorg Chem 2022; 27:239-248. [PMID: 35064831 PMCID: PMC8907109 DOI: 10.1007/s00775-022-01924-9] [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: 11/12/2021] [Accepted: 12/30/2021] [Indexed: 11/03/2022]
Abstract
AbstractAlthough genomic DNA is the primary target of anticancer platinum-based drugs, interactions with proteins also play a significant role in their overall activity. In this study, competitive binding of cisplatin with an oligonucleotide and two peptides corresponding to segments of H2A and H2B histone proteins was investigated by mass spectrometry. Following the determination of the cisplatin binding sites on the oligonucleotide and peptides by tandem mass spectrometry, competitive binding was studied and transfer of platinum fragments from the platinated peptides to the oligonucleotide explored. In conjunction with previous studies on the nucleosome, the results suggest that all four of the abundant histone proteins serve as a platinum drug reservoir in the cell nucleus, providing an adduct pool that can be ultimately transferred to the DNA.
Graphical abstract
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2
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Moon HM, Park JS, Lee IB, Kang YI, Jung HJ, An D, Shin Y, Kim MJ, Kim HI, Song JJ, Kim J, Lee NK, Hong SC. Cisplatin fastens chromatin irreversibly even at a high chloride concentration. Nucleic Acids Res 2021; 49:12035-12047. [PMID: 34865121 PMCID: PMC8643659 DOI: 10.1093/nar/gkab922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/12/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
Cisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.
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Affiliation(s)
- Hyeon-Min Moon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Jin-Sung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | - Il-Buem Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Young-Im Kang
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Hae Jun Jung
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Dongju An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yumi Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Min Ji Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul 05006, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
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3
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Rose PK, Watkins NH, Yao X, Zhang S, Mancera-Ortiz IY, Sloop JT, Donati GL, Day CS, Bierbach U. Effect of the nonleaving groups on the cellular uptake and cytotoxicity of platinum-acridine anticancer agents. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.04.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Lajous H, Riva R, Lelièvre B, Tétaud C, Avril S, Hindré F, Boury F, Jérôme C, Lecomte P, Garcion E. Hybrid Gd3+/cisplatin cross-linked polymer nanoparticles enhance platinum accumulation and formation of DNA adducts in glioblastoma cell lines. Biomater Sci 2018; 6:2386-2409. [DOI: 10.1039/c8bm00346g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
New hybrid nanoparticles permitted MRI monitoring of a cisplatin infusion while enhancing drug accumulation and DNA adduct formation in glioblastoma cells.
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Affiliation(s)
- Hélène Lajous
- CRCINA
- INSERM
- Université de Nantes
- Université d'Angers
- Angers
| | - Raphaël Riva
- Center for Education and Research on Macromolecules (CERM)
- CESAM Research Unit
- University of Liège
- B-4000 Liège
- Belgium
| | - Bénédicte Lelièvre
- Centre régional de pharmacovigilance
- Laboratoire de pharmacologie-toxicologie
- CHU Angers
- F-49100 Angers
- France
| | - Clément Tétaud
- CRCINA
- INSERM
- Université de Nantes
- Université d'Angers
- Angers
| | - Sylvie Avril
- CRCINA
- INSERM
- Université de Nantes
- Université d'Angers
- Angers
| | | | - Frank Boury
- CRCINA
- INSERM
- Université de Nantes
- Université d'Angers
- Angers
| | - Christine Jérôme
- Center for Education and Research on Macromolecules (CERM)
- CESAM Research Unit
- University of Liège
- B-4000 Liège
- Belgium
| | - Philippe Lecomte
- Center for Education and Research on Macromolecules (CERM)
- CESAM Research Unit
- University of Liège
- B-4000 Liège
- Belgium
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6
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Murray BS, Babak MV, Hartinger CG, Dyson PJ. The development of RAPTA compounds for the treatment of tumors. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.06.014] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Zhu G, Song L, Lippard SJ. Visualizing inhibition of nucleosome mobility and transcription by cisplatin-DNA interstrand crosslinks in live mammalian cells. Cancer Res 2013; 73:4451-60. [PMID: 23695549 DOI: 10.1158/0008-5472.can-13-0198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cisplatin is a widely used anticancer drug that acts by binding DNA and causing the formation of intrastrand and interstrand (ICL) crosslinks, but the precise downstream effects of the latter damage are not well understood. In this study, we investigated the influence of cisplatin ICLs on synthetic nucleosomes that were platinated in a site-specific manner in vitro and on gene transcription in live mammalian cells. Nucleosome core particles that we constructed contained site-specific cisplatin 5'-d(G*pC)/5'-d(G*pC) ICLs, where the asterisk denotes the platinated nucleoside, to examine the influence of platinum lesions on the dynamic behavior of nucleosomes in solution. A cisplatin ICL, but not a 1,2-d(GpG) crosslink, significantly inhibited ATP-independent histone octamer-DNA sliding. We also used a novel linearization-recircularization strategy described here to synthesize mammalian expression vectors containing site-specific cisplatin ICLs. Plasmid vectors were tested in live mammalian cells to study the transcription inhibition effects of cisplatin ICLs in the context of two different repair backgrounds. Cisplatin ICLs inhibit transcription as effectively as 1,2-d(GpG) crosslinks. We determined that nucleotide excision repair plays a key role in the removal of cisplatin ICLs, acting in a replication-independent fashion. We also found that loss of mismatch repair function dramatically attenuates the transcription inhibition effects by cisplatin ICLs but not 1,2-d(GpG) intrastrand crosslinks. Our results revealed the unique properties of cisplatin ICLs on nucleosome mobility and on transcription, and they defined how these adducts act in a manner completely different from that used for cisplatin 1,2-d(GpG) crosslinks. These new findings provide direct support for a role of ICLs in the pharmacologic activities of cisplatin, despite the lower frequency of their formation.
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Affiliation(s)
- Guangyu Zhu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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8
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Minor Groove Binder Distamycin Remodels Chromatin but Inhibits Transcription. PLoS One 2013; 8:e57693. [PMID: 23460895 PMCID: PMC3584068 DOI: 10.1371/journal.pone.0057693] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
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9
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Anticancer metallodrug research analytically painting the "omics" picture--current developments and future trends. Anal Bioanal Chem 2012; 405:1791-808. [PMID: 23070042 DOI: 10.1007/s00216-012-6450-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 09/14/2012] [Accepted: 09/21/2012] [Indexed: 01/27/2023]
Abstract
Anticancer metallodrug development has for a long time been characterised by the similarity of new drug candidates to cisplatin and DNA as the primary target. Recent advances in bioanalytical techniques with high sensitivity and selectivity have revealed that metal-based drugs can undergo a wide range of biomolecular interactions beyond DNA and have generated interest in proteins as possible targets for metallodrugs. In fact, implementation of metallomics approaches that are able to reveal the fate of the compounds in biological systems can help to move drug development towards more targeted and rational design of novel metallodrugs. Additionally, proteomic screening and gene expression analysis can provide insight into physiological response to drug treatment and identify the reasons for drug resistance. Herein, we review selected applications which led to a better understanding of the mode of action of clinically established metal-based anticancer agents and novel metallodrug candidates.
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10
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Tai HC, Brodbeck R, Kasparkova J, Farrer NJ, Brabec V, Sadler PJ, Deeth RJ. Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)2] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]. Inorg Chem 2012; 51:6830-41. [DOI: 10.1021/ic3005745] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hui-Chung Tai
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Ralf Brodbeck
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Jana Kasparkova
- The Institute of
Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 61265 Brno, Czech Republic
| | - Nicola J. Farrer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Viktor Brabec
- The Institute of
Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 61265 Brno, Czech Republic
| | - Peter J. Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Robert J. Deeth
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
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Wu B, Davey GE, Nazarov AA, Dyson PJ, Davey CA. Specific DNA structural attributes modulate platinum anticancer drug site selection and cross-link generation. Nucleic Acids Res 2011; 39:8200-12. [PMID: 21724603 PMCID: PMC3185412 DOI: 10.1093/nar/gkr491] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heavy metal compounds have toxic and medicinal potential through capacity to form strong specific bonds with macromolecules, and the interaction of platinum drugs at the major groove nitrogen atom of guanine bases primarily underlies their therapeutic activity. By crystallographic analysis of transition metal-and in particular platinum compound-DNA site selectivity in the nucleosome core, we establish that steric accessibility, which is controlled by specific structural parameters of the double helix, modulates initial guanine-metal bond formation. Moreover, DNA conformational features can be linked to both similarities and distinctions in platinum drug adduct formation between the naked and nucleosomal DNA states. Notably, structures that facilitate initial platinum-guanine bond formation can oppose cross-link generation, rationalizing the occurrence of long-lived therapeutically ineffective monofunctional adducts. These findings illuminate DNA structure-dependent reactivity and provide a novel framework for understanding metal-double helix interactions, which should facilitate the development of improved chromatin-targeting medicinal agents.
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Affiliation(s)
- Bin Wu
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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12
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Todd RC, Lippard SJ. Consequences of cisplatin binding on nucleosome structure and dynamics. ACTA ACUST UNITED AC 2011; 17:1334-43. [PMID: 21168769 DOI: 10.1016/j.chembiol.2010.10.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/06/2010] [Accepted: 10/18/2010] [Indexed: 11/15/2022]
Abstract
The effects of cisplatin binding to DNA were explored at the nucleosome level to incorporate key features of the eukaryotic nuclear environment. An X-ray crystal structure of a site-specifically platinated nucleosome carrying a 1,3-cis-{Pt(NH₃)₂}²+-d(GpTpG) intrastrand cross-link reveals the details of how this adduct dictates the rotational positioning of DNA in the nucleosome. Results from in vitro nucleosome mobility assays indicate that a single platinum adduct interferes with ATP-independent sliding of DNA around the octamer core. Data from in vitro transcription experiments suggest that RNA polymerases can successfully navigate along cisplatin-damaged DNA templates that contain nucleosomes, but stall when the transcription elongation complex physically contacts a platinum cross-link located on the template strand. These results provide information about the effects of cisplatin binding to nuclear DNA and enhance our understanding of the mechanism of transcription inhibition by platinum anticancer compounds.
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Affiliation(s)
- Ryan C Todd
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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13
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Bounaix Morand du Puch C, Barbier E, Kraut A, Couté Y, Fuchs J, Buhot A, Livache T, Sève M, Favier A, Douki T, Gasparutto D, Sauvaigo S, Breton J. TOX4 and its binding partners recognize DNA adducts generated by platinum anticancer drugs. Arch Biochem Biophys 2010; 507:296-303. [PMID: 21184731 DOI: 10.1016/j.abb.2010.12.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/12/2010] [Accepted: 12/17/2010] [Indexed: 10/18/2022]
Abstract
Platinating agents are commonly prescribed anticancer drugs damaging DNA. Induced lesions are recognized by a wide range of proteins. These are involved in cellular mechanisms such as DNA repair, mediation of cytotoxicity or chromatin remodeling. They therefore constitute crucial actors to understand pharmacology of these drugs. To expand our knowledge about this subproteome, we developed a ligand fishing trap coupled to high throughput proteomic tools. This trap is made of damaged plasmids attached to magnetic beads, and was exposed to cell nuclear extracts. Retained proteins were identified by nanoHPLC coupled to tandem mass spectrometry. This approach allowed us to establish a list of 38 proteins interacting with DNA adducts generated by cisplatin, oxaliplatin and satraplatin. Some of them were already known interactome members like high mobility group protein 1 (HMGB1) or the human upstream binding factor (hUBF), but we also succeeded in identifying unexpected proteins such as TOX HMG box family member 4 (TOX4), phosphatase 1 nuclear targeting subunit (PNUTS), and WD repeat-containing protein 82 (WDR82), members of a recently discovered complex. Interaction between TOX4 and platinated DNA was subsequently validated by surface plasmon resonance imaging (SPRi). These interactions highlight new cellular responses to DNA damage induced by chemotherapeutic agents.
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Affiliation(s)
- Christophe Bounaix Morand du Puch
- CEA Grenoble, INAC, SCIB (UMR E_3 CEA-Université Joseph Fourier, CNRS FRE3200)-Laboratoire Lésions des Acides Nucléiques, 17 Rue des Martyrs, 38054 Grenoble Cedex 09, France
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14
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Arnesano F, Belviso BD, Caliandro R, Falini G, Fermani S, Natile G, Siliqi D. Crystallographic Analysis of Metal-Ion Binding to Human Ubiquitin. Chemistry 2010; 17:1569-78. [DOI: 10.1002/chem.201001617] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Indexed: 01/24/2023]
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15
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Ong MS, Vasudevan D, Davey CA. Divalent metal- and high mobility group N protein-dependent nucleosome stability and conformation. J Nucleic Acids 2010; 2010:143890. [PMID: 21188164 PMCID: PMC3005839 DOI: 10.4061/2010/143890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 09/29/2010] [Indexed: 11/21/2022] Open
Abstract
High mobility group N proteins (HMGNs) bind specifically to the nucleosome core and act as chromatin unfolding and activating factors. Using an all-Xenopus system, we found that HMGN1 and HMGN2 binding to nucleosomes results in distinct ion-dependent conformation and stability. HMGN2 association with nucleosome core particle or nucleosomal array in the presence of divalent metal triggers a reversible transition to a species with much reduced electrophoretic mobility, consistent with a less compact state of the nucleosome. Residues outside of the nucleosome binding domain are required for the activity, which is also displayed by an HMGN1 truncation product lacking part of the regulatory domain. In addition, thermal denaturation assays show that the presence of 1 mM Mg2+> or Ca2+ gives a reduction in nucleosome core terminus stability, which is further substantially diminished by the binding of HMGN2 or truncated HMGN1. Our findings emphasize the importance of divalent metals in nucleosome dynamics and suggest that the differential biological activities of HMGNs in chromatin activation may involve different conformational alterations and modulation of nucleosome core stability.
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Affiliation(s)
- Michelle S Ong
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Ghosh S, Majumder P, Pradhan SK, Dasgupta D. Mechanism of interaction of small transcription inhibitors with DNA in the context of chromatin and telomere. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:795-809. [PMID: 20638489 DOI: 10.1016/j.bbagrm.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/23/2010] [Accepted: 06/30/2010] [Indexed: 01/13/2023]
Abstract
Small molecules from natural and synthetic sources have long been employed as human drugs. The transcription inhibitory potential of one class of these molecules has paved their use as anticancer drugs. The principal mode of action of these molecules is via reversible interaction with genomic DNA, double and multiple stranded. In this article we have revisited the mechanism of the interaction in the context of chromatin and telomere. The established modes of association of these molecules with double helical DNA provide a preliminary mechanism of their transcription inhibitory potential, but the scenario assumes a different dimension when the genomic DNA is associated with proteins in the transcription apparatus of both prokaryotic and eukaryotic organisms. We have discussed this altered scenario as a prelude to understand the chemical biology of their action in the cell. For the telomeric quadruplex DNA, we have reviewed the mechanism of their association with the quadruplex and resultant cellular consequence.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhan Nagar, Kolkata Pin, 700064, India
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17
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Ahmad S. Platinum-DNA interactions and subsequent cellular processes controlling sensitivity to anticancer platinum complexes. Chem Biodivers 2010; 7:543-66. [PMID: 20232326 DOI: 10.1002/cbdv.200800340] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Platinum-based compounds are widely used as chemotherapeutics for the treatment of a variety of cancers. The anticancer activity of cisplatin and other platinum drugs is believed to arise from their interaction with DNA. Several cellular pathways are activated in response to this interaction, which include recognition by high-mobility group and repair proteins, translesion synthesis by polymerases, and induction of apoptosis. The apoptotic process is regulated by activation of caspases, p53 gene, and several proapoptotic and antiapoptotic proteins. Such cellular processing eventually leads to an inhibition of the replication or transcription machinery of the cell. Deactivation of platinum drugs by thiols, increased nucleotide excision repair of Pt-DNA adducts, decreased mismatch repair, and defective apoptosis result in resistance to platinum therapy. The differences in cytotoxicity of various platinum complexes are attributed to the differential recognition of their adducts by cellular proteins. Cisplatin and oxaliplatin both produce mainly 1,2-GG intrastrand cross-links as major adducts, but oxaliplatin is found to be more active particularly against cisplatin-resistant tumor cells. Mismatch repair and replicative bypass appear to be the processes most likely involved in differentiating the molecular responses to these two agents. This review describes the formation of Pt-DNA adducts, their interaction with cellular components, and biological effects of this interaction.
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Affiliation(s)
- Saeed Ahmad
- Department of Chemistry, University of Engineering and Technology, Lahore 54890, Pakistan.
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Mohideen K, Muhammad R, Davey CA. Perturbations in nucleosome structure from heavy metal association. Nucleic Acids Res 2010; 38:6301-11. [PMID: 20494975 PMCID: PMC2952864 DOI: 10.1093/nar/gkq420] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co2+ and Ni2+ preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb+ and Cs+ are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn2+ the aggressive coordination of Co2+ and Ni2+ to guanine bases is observed to induce a shift in histone–DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These ‘softer’ transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co2+ and Ni2+.
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Affiliation(s)
- Kareem Mohideen
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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Abstract
Cisplatin, carboplatin, and oxaliplatin are three FDA-approved members of the platinum anticancer drug family. These compounds induce apoptosis in tumor cells by binding to nuclear DNA, forming a variety of structural adducts and triggering cellular responses, one of which is the inhibition of transcription. In this report we present (i) a detailed review of the structural investigations of various Pt-DNA adducts and the effects of these lesions on global DNA geometry; (ii) research detailing inhibition of cellular transcription by Pt-DNA adducts; and (iii) a mechanistic analysis of how DNA structural distortions induced by platinum damage may inhibit RNA synthesis in vivo. A thorough understanding of the molecular mechanism of action of platinum antitumor agents will aid in the development of new compounds in the family.
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Affiliation(s)
- Ryan C. Todd
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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