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Liu S, Liang A, Wu K, Zeng W, Luo Q, Wang F. Binding of Organometallic Ruthenium Anticancer Complexes to DNA: Thermodynamic Base and Sequence Selectivity. Int J Mol Sci 2018; 19:ijms19072137. [PMID: 30041439 PMCID: PMC6073332 DOI: 10.3390/ijms19072137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 11/16/2022] Open
Abstract
Organometallic ruthenium(II) complexes [(η⁶-arene)Ru(en)Cl][PF₆] (arene = benzene (1), p-cymene (2), indane (3), and biphenyl (4); en = ethylenediamine) are promising anticancer drug candidates both in vitro and in vivo. In this paper, the interactions between ruthenium(II) complexes and 15-mer single- and double-stranded oligodeoxynucleotides (ODNs) were thermodynamically investigated using high performance liquid chromatography (HPLC) and electrospray ionization mass spectroscopy (ESI-MS). All of the complexes bind preferentially to G₈ on the single strand 5'-CTCTCTT₇G₈T₉CTTCTC-3' (I), with complex 4 containing the most hydrophobic ligand as the most reactive one. To the analogs of I (changing T₇ and/or T₉ to A and/or C), complex 4 shows a decreasing affinity to the G₈ site in the following order: -AG₈T- (K: 5.74 × 10⁴ M-1) > -CG₈C- > -TG₈A- > -AG₈A- > -AG₈C- > -TG₈T- (I) ≈ -CG₈A- (K: 2.81 × 10⁴ M-1). In the complementary strand of I, the G bases in the middle region are favored for ruthenation over guanine (G) bases in the end of oligodeoxynucleotides (ODNs). These results indicate that both the flanking bases (or base sequences) and the arene ligands play important roles in determining the binding preference, and the base- and sequence-selectivity, of ruthenium complex in binding to the ODNs.
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Affiliation(s)
- Suyan Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Aihua Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Kui Wu
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Wenjuan Zeng
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Centre for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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Tai TB, Nhat PV. A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.05.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wu K, Liu S, Luo Q, Hu W, Li X, Wang F, Zheng R, Cui J, Sadler PJ, Xiang J, Shi Q, Xiong S. Thymines in Single-Stranded Oligonucleotides and G-Quadruplex DNA Are Competitive with Guanines for Binding to an Organoruthenium Anticancer Complex. Inorg Chem 2013; 52:11332-42. [DOI: 10.1021/ic401606v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kui Wu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Suyan Liu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Qun Luo
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Wenbing Hu
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Xianchan Li
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Fuyi Wang
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
| | - Renhui Zheng
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing 100190, P. R. China
| | - Jie Cui
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Peter J. Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4
7AL, United Kingdom
| | - Junfeng Xiang
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qiang Shi
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Beijing 100190, P. R. China
| | - Shaoxiang Xiong
- Beijing National
Laboratory
for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- CAS Key Laboratory of Analytical
Chemistry for Living Biosystems, Beijing Centre for Mass Spectrometry, Beijing 100190, P. R. China
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Nguyen TH, Arnesano F, Scintilla S, Rossetti G, Ippoliti E, Carloni P, Natile G. Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. J Chem Theory Comput 2012; 8:2912-20. [DOI: 10.1021/ct300167m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Trung Hai Nguyen
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Fabio Arnesano
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Simone Scintilla
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Statistical and Biological Physics Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,
I-34136 Trieste, Italy
| | - Giovanni Natile
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
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Fu Q, Zhou L, Li J. Binding of anticancer drug Ru(η 6 -C6H5(CH2)2OH)Cl2(DAPTA) to DNA purine bases and amino acid residues: a theoretical study. Struct Chem 2012. [DOI: 10.1007/s11224-012-0003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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A theoretical study on transition state of the antitumor drug: Gold(III) dithiocarbamate derivative interaction with cysteine and DNA purine bases. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Zhou L. Computational study on the mechanisms of action of the potential anticancer drug trans-isopropylaminedimethylaminedichloroplatinum (trans-IPADMADP) and its cis isomer with DNA purine bases. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.05.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Suchánková T, Kubíček K, Kašpárková J, Brabec V, Kozelka J. Platinum-DNA interstrand crosslinks: molecular determinants of bending and unwinding of the double helix. J Inorg Biochem 2011; 108:69-79. [PMID: 22019433 DOI: 10.1016/j.jinorgbio.2011.09.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 09/09/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
Platinum diamine complexes are able to crosslink the guanines of d(GC)(2) dinucleotides within double-stranded DNA. The interstrand crosslink thus formed causes a bend of the double helix toward the minor groove and the helical sense changes locally to left-handed, resulting in a considerable unwinding. The bend and unwinding angles have been shown to depend on the platinum ligands. Here, we have used molecular dynamics simulations to investigate the DNA 20-mer d(C(1)T(2)C(3)T(4)C(5)C(6)T(7)T(8)G*(9)C(10)T(11)C(12)T(13)C(14)C(15)T(16)T(17)C(18)T(19)C(20))-d(G(21)A(22)G(23)A(24)A(25)G(26)G(27)A(28)G(29)A(30)G*(31)C(32)A(33)A(34)G(35)G(36)A(37)G(38)A(39)G(40)) with the G* guanines crosslinked by cis-Pt(NH(3))(2)(2+), Pt(R,R-DACH)(2+), or Pt(S,S-DACH)(2+). Previous investigations on cisplatin interstrand adducts indicated that the structure is similar in solid state and in solution; thus, we used the reported X-ray structure of a cisplatin adduct as a starting model. Replacing in the MD-relaxed model for the DNA duplex crosslinked with cis-Pt(NH(3))(2)(2+) the two NH(3) platinum ligands by R,R-DACH or S,S-DACH led to clashes between the DACH residue and the deoxyribose of C(12). Confrontation of MD-derived models with gel shift measurements suggested that these clashes are avoided differently in the adducts of Pt(R,R-DACH)(2+)versus Pt(S,S-DACH)(2+). The R,R-isomer avoids the clash by untwisting the T(11)/A(30)-C(12)/G(29) step, thus increasing the global unwinding. In contrast, the S,S-isomer modifies the shift and slide parameters of this step, which dislocates the helical axis and enhances the bend angle. The clash that leads to the differentiation of the structures as a function of the diamine ligand is related to a hydrogen bond between the platinum complex and the T(11) base and could be characteristic of interstrand crosslinks at d(pyG*Cpy)-d(puG*Cpu) sequences.
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Affiliation(s)
- Tereza Suchánková
- Department of Biophysics, Faculty of Sciences, Palacky University, Olomouc, Czech Republic
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9
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Chapman EG, Hostetter AA, Osborn MF, Miller AL, DeRose VJ. Binding of kinetically inert metal ions to RNA: the case of platinum(II). Met Ions Life Sci 2011; 9:347-77. [PMID: 22010278 PMCID: PMC4080900 DOI: 10.1039/9781849732512-00347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter several aspects of Pt(II) are highlighted that focus on the properties of Pt(II)-RNA adducts and the possibility that they influence RNA-based processes in cells. Cellular distribution of Pt(II) complexes results in significant platination of RNA, and localization studies find Pt(II) in the nucleus, nucleolus, and a distribution of other sites in cells. Treatment with Pt(II) compounds disrupts RNA-based processes including enzymatic processing, splicing, and translation, and this disruption may be indicative of structural changes to RNA or RNA-protein complexes. Several RNA-Pt(II) adducts have been characterized in vitro by biochemical and other methods. Evidence for Pt(II) binding in non-helical regions and for Pt(II) cross-linking of internal loops has been found. Although platinated sites have been identified, there currently exists very little in the way of detailed structural characterization of RNA-Pt(II) adducts. Some insight into the details of Pt(II) coordination to RNA, especially RNA helices, can be gained from DNA model systems. Many RNA structures, however, contain complex tertiary folds and common, purine-rich structural elements that present suitable Pt(II) nucleophiles in unique arrangements which may hold the potential for novel types of platinum-RNA adducts. Future research aimed at structural characterization of platinum-RNA adducts may provide further insights into platinum-nucleic acid binding motifs, and perhaps provide a rationale for the observed inhibition by Pt(II) complexes of splicing, translation, and enzymatic processing.
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Affiliation(s)
- Erich G. Chapman
- Department of Chemistry University of Oregon Eugene OR 97403 USA
| | | | - Maire F. Osborn
- Department of Chemistry University of Oregon Eugene OR 97403 USA
| | - Amanda L. Miller
- Department of Chemistry University of Oregon Eugene OR 97403 USA
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10
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Sanz Miguel PJ, Roitzsch M, Yin L, Lax PM, Holland L, Krizanovic O, Lutterbeck M, Schürmann M, Fusch EC, Lippert B. On the many roles of NH3 ligands in mono- and multinuclear complexes of platinum. Dalton Trans 2009:10774-86. [PMID: 20023907 DOI: 10.1039/b916537a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the NH(3) ligands in the highly successful antitumour agents cisplatin and carboplatin is not fully understood. Suggestions that the ammonia ligands are involved in target recognition through hydrogen bond formation, e.g. with guanine-O6, have been questioned. Here, we review the roles and functions of NH(3) ligands of cis-PtCl(2)(NH(3))(2) and likewise of its trans-isomer in complexes with model nucleobases as well as other N-heterocyclic ligands. Specifically, their roles in hydrogen bonding interactions with nucleobases as well as anions, the influence on acid-base properties of co-ligands, their involvement in condensation reactions, as well as a variety of displacement reactions will be examined. As a result, it can be stated that the ammonia ligands in cis- and trans-Pt(II)(NH(3))(2) entities display additional features to those generally discussed in the last four decades since the discovery of the antitumour activity of cisplatin.
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Téletchéa S, Skauge T, Sletten E, Kozelka J. Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2009; 15:12320-37. [DOI: 10.1002/chem.200901158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Hostetter AA, Chapman EG, DeRose VJ. Rapid cross-linking of an RNA internal loop by the anticancer drug cisplatin. J Am Chem Soc 2009; 131:9250-7. [PMID: 19566097 DOI: 10.1021/ja809637e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cisplatin is the most prominent member of a series of platinum(II) antitumor drugs that demonstrate activity based on binding to adjacent purines on genomic DNA. The interactions between cisplatin and alternate biomolecules, including chemically similar RNA, are less understood than are those for DNA. In order to investigate potential implications of platinum(II) drug binding to a structurally complex RNA, we have characterized the reaction between cisplatin and the internal loop of a 41-nucleotide subdomain derived from the U2:U6 spliceosomal RNAs. This "BBD" RNA subdomain consists of a hairpin structure containing a purine-rich asymmetric internal loop. Aquated cisplatin is found to cross-link G nucleobases on opposing sides of the internal loop, forming an intramolecular internal loop cross-link in BBD and an analogous intermolecular cross-link in a two-piece construct containing the same internal loop sequence. The two opposing guanine residues involved in the cross-link were identified via limited alkaline hydrolysis. The kinetics of aquated cisplatin binding to the BBD RNA, a related RNA hairpin, and its DNA hairpin analogue were investigated in an ionic background of 0.1 M NaNO(3) and 1 mM Mg(NO(3))(2). Both BBD and the RNA hairpin react 5-6-fold faster than the DNA hairpin, with calculated second-order rate constants of 2.0(2), 1.7(3), and 0.33(3) M(-1) s(-1), respectively, at 37 degrees C, pH 7.8. MALDI-MS data corroborate the biochemical studies and support a model in which kinetically preferred platinum binding sites compete with less reactive sites in these oligonucleotides. Taken together, these data indicate that cisplatin treatment has potential to create internal loop and other unusual cross-links in structurally complex RNAs, on a time scale that is relevant for RNA-dependent biological processes.
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Kozelka J. Molecular origin of the sequence-dependent kinetics of reactions between cisplatin derivatives and DNA. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.04.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Zhou L. Theoretical Analysis on the Transition State of the Anticancer Drug trans-[PtCl2(isopropylamine)2] and Its cis Isomer Binding to DNA Purine Bases. J Phys Chem B 2009; 113:2110-27. [DOI: 10.1021/jp806661g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Lixin Zhou
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P. R. China
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Hägerlöf M, Hedman H, Elmroth SKC. Platination of the siRNA sense-strand modulates both efficacy and selectivity in vitro. Biochem Biophys Res Commun 2007; 361:14-9. [PMID: 17632077 DOI: 10.1016/j.bbrc.2007.06.131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 06/19/2007] [Indexed: 11/17/2022]
Abstract
The use of short interfering RNAs (siRNA) for selective suppression of protein production has rapidly become a commonly used technique for transient modulation of protein levels. In the present paper, we investigate whether introduction of platinated bases in the sense strand can be used to modulate the efficacy of siRNAs. Four different siRNAs were studied, all targeting the initial AU-rich 3' UTR of Wnt-5a mRNA. The siRNAs were characterized with respect to melting properties and translational inhibitory effect in vitro using luciferase as a reporter gene. The translation inhibition studies reveal that all platinated siRNA remain efficient. For an siRNA with partial complementarity to the luciferase gene, platination was shown to reduce the off-target effects. All siRNAs were found to be active in cellular in vitro translation systems, reaching suppression levels well above 80% for the majority of siRNAs investigated.
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Affiliation(s)
- Margareta Hägerlöf
- Biokemi, Kemicentrum, Lunds Universitet, Box 124, SE-221 00 Lund, Sweden
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Vinje J, Sletten E. Internal versus terminal metalation of double-helical oligodeoxyribonucleotides. Chemistry 2007; 12:676-88. [PMID: 16208725 DOI: 10.1002/chem.200500731] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The formation of adducts between cis-[Pt(NH(3))(2)Cl(2)], Zn(II), and Mn(II) and double-stranded oligodeoxynucleotides was studied by 1D and 2D (1)H, (31)P, and (15)N NMR spectroscopy. For labile adducts involving Zn(II) and Mn(II), both (1)H chemical shifts (Zn(II)) and (1)H line-broadening effects (Mn(II)) showed that in the hexamer [d(GGCGCC)](2) I, the terminal G(1)-N7 is the exclusive binding site, while for the dodecamer [d(GGTACCGGTACC)](2) II, which contains both a terminal and internal GG pair, the preference for metal binding is the internal guanine G(7). Zn(II) binding to II was confirmed by natural-abundance 2D [(1)H,(15)N] HMBC NMR spectroscopy, which unambiguously showed that G(7)-N7 is the preferred binding site. The long duplex [d(GGTATATATACCGGTATATATACC)](2) III was expected to have a more pronounced accumulation of electrostatic potential towards the central part of the sequence (vs the terminal part) than does II. However, the Zn(II) titration of III showed no increase in coordination with the internal Gs (vs the terminal Gs), compared with what was observed for II. The reaction between the nonlabile metal complex cis-[PtCl(2)((15)NH(3))(2)] (cisplatin) and II showed a slight preference for the internal GG pair over the terminal GG pair. However, when the diaqua form of cisplatin cis-[Pt((15)NH(3))(2)(H(2)O)(2)] was reacted with II a more pronounced binding preference for the internal GG pair was observed.
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Affiliation(s)
- Jo Vinje
- Centre of Pharmacy, Department of Chemistry, University of Bergen, Norway.
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17
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Gómez K, González G, Martínez M, Mendoza C, Sienra B. Absence of phosphate hydrolysis in the nucleotide substitution reaction on cis-[Co(H2O)2(cyclen)]3+ at physiological pH: Importance of hydrogen-bonding and conjugate base-catalysis. Polyhedron 2006. [DOI: 10.1016/j.poly.2006.06.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ourliac Garnier I, Bombard S. GG sequence of DNA and the human telomeric sequence react with cis-diammine-diaquaplatinum at comparable rates. J Inorg Biochem 2006; 101:514-24. [PMID: 17224184 DOI: 10.1016/j.jinorgbio.2006.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 11/07/2006] [Accepted: 11/10/2006] [Indexed: 11/22/2022]
Abstract
G-quadruplex structures of telomeric sequences are of growing interest because they inhibit telomerase, an enzyme involved in the maintenance of telomere length of cancer cells. As we have shown previously, the antiparallel structure of G-quadruplexes can be cross-linked in vitro by the anti-tumour drug cisplatin. The question arises whether platination of quadruplex structures of human telomeric sequences by cisplatin could be relevant from a biological point of view. Therefore, we have compared the kinetics of reactions of the diaqua form of cisplatin, cis-[Pt(NH(3))(2)(H(2)O)(2)](2+), with the human telomeric quadruplex structure, a duplex DNA and a single-stranded DNA containing one specific platination GG site. The ratio between the platination rate constants was obtained using two intramolecular competition experiments: either a construct with a junction between duplex DNA containing a unique GG platination site and the quadruplex structure of the human telomeric sequence AG(3)(T(2)AG(3))(3), or a construct with a junction between duplex DNA and a single strand containing each a unique GG platination site. Those competition experiments allowed us to conclude that the platination of the quadruplex is favoured over that of the GG duplex by a factor of about two whereas the GG duplex is platinated three times faster than the GG single strand.
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Affiliation(s)
- Isabelle Ourliac Garnier
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601, Université René Descartes, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
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19
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Vinje J, Sletten E, Kozelka J. Influence of dT20 and [d(AT)10]2 on cisplatin hydrolysis studied by two-dimensional [1H,15N] HMQC NMR spectroscopy. Chemistry 2006; 11:3863-71. [PMID: 15827978 DOI: 10.1002/chem.200500002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The influence of the presence of DNA on the kinetics of cisplatin (cis-[PtCl2(NH3)2]) aquation (replacement of Cl- by H2O) and anation (replacement of H2O by Cl-) involved in the hydrolysis of cisplatin have been determined by two-dimensional [1H,15N] HMQC NMR spectroscopy. Single-stranded dT20 and double-stranded [d(AT)10]2 oligonucleotides were used as DNA models, avoiding guanines which are known to react rapidly with aquated cisplatin forms. Reactions starting from cis-[PtCl2(15NH3)2], or from a stoichiometric mixture of cis-[Pt(15NH3)2(H2O)2]2+ and Cl- (all 0.5 mM Pt(II); in ionic strength, adjusted to 0.095 M or 0.011 M with NaClO4, pH between 3.0 and 4.0) were followed in an NMR tube in both the absence and presence of 0.7 mM dT20 or [d(AT)10]2. In the presence of dT20, we observed a slight and ionic-strength-independent decrease (15-20 %) of the first aquation rate constant, and a more significant decrease of the second anation rate constant. The latter was more important at low ionic strength, and can be explained by efficient condensation of cis-[Pt(15NH3)2(H2O)2]2+ on the surface of single-stranded DNA, in a region depleted of chloride anions. At low ionic strength, we observed an additional set of [1H,15N] HMQC spectral signals indicative of an asymmetric species of PtN2O2 coordination, and we assigned them to phosphate-bound monoadducts of cis-[Pt(15NH3)2(H2O)2]2+. Double-stranded [d(AT)10]2 slowed down the first aquation step also by approximately 15 %; however, we could not determine the influence on the second hydrolysis step because of a significant background reaction with cis-[Pt(NH3)2(H2O)2]2+.
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Affiliation(s)
- Jo Vinje
- Department of Chemistry, University of Bergen, Allégt. 41, 5007 Bergen, Norway.
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Romerosa A, Campos-Malpartida T, Lidrissi C, Saoud M, Serrano-Ruiz M, Peruzzini M, Garrido-Cárdenas JA, García-Maroto F. Synthesis, Characterization, and DNA Binding of New Water-Soluble Cyclopentadienyl Ruthenium(II) Complexes Incorporating Phosphines. Inorg Chem 2006; 45:1289-98. [PMID: 16441141 DOI: 10.1021/ic051053q] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The new water-soluble ruthenium(II) chiral complexes [RuCpX(L)(L')](n+) (X = Cl, I. L = PPh3; L' = PTA, mPTA; L = L' = PTA, mPTA) (PTA = 1,3,5-triaza-7-phosphaadamantane; mPTA = N-methyl-1,3,5-triaza-7-phosphaadamantane) have been synthesized and characterized by NMR and IR spectroscopy and elemental analysis. The salt mPTA(OSO2CF3) was also prepared and fully characterized by spectroscopic techniques. X-ray crystal structures of [RuClCp(PPh3)(PTA)] (2), [RuCpI(PPh3)(PTA)] (3), and [RuCpI(mPTA)(PPh3)](OSO2CF3) (9) have been determined. The binding properties toward DNA of the new hydrosoluble complexes have been studied using the mobility shift assay. The ruthenium chloride complexes interact with DNA depending on the hydrosoluble phosphine bonded to the metal, while the corresponding compounds with iodide, [RuCpI(PTA)2] (1), [RuCpI(PPh3)(PTA)] (3), [RuCpI(mPTA)2](OSO2CF3)2 (6), and [RuCpI(mPTA)(PPh3)](OSO2CF3) (9), do not bind to DNA.
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Affiliation(s)
- Antonio Romerosa
- Area de Química Inorgánica, Facultad de Ciencias, Universidad de Almería, Almería, Spain.
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21
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Deubel DV. Factors governing the kinetic competition of nitrogen and sulfur ligands in cisplatin binding to biological targets. J Am Chem Soc 2004; 126:5999-6004. [PMID: 15137764 DOI: 10.1021/ja0499602] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The kinetic competition of sulfur and nitrogen nucleophiles L in the substitution reactions of cisplatin derivatives, cis-[Pt(II)(NH(3))(2)(X)(OH(2))](n)(+) + L --> cis-[Pt(II)(NH(3))(2)(X)(L)](m)(+) + H(2)O (X = Cl(-), H(2)O), has been studied using density functional theory and continuum dielectric calculations. The calculations reveal an intrinsic kinetic preference of platinum(II) for nitrogen over sulfur ligands. However, biologically relevant substituents can mask this preference for nitrogen nucleophiles. Investigation of the activation free energies of the substitution reactions in dependence of the dielectric constant epsilon demonstrates the microenvironment to be crucial in the binding of cisplatin to its intracellular targets. The fused aromatic heterocycle of guanine stabilizes the transition state for platination at a smaller epsilon more efficiently than do the functional groups of amino acid residues. The results of this work suggest a relatively facile platination of guanine-N7 sites of DNA in regions of low epsilon, particularly in the proximity of histone cores.
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Affiliation(s)
- Dirk V Deubel
- Department of Chemistry and Applied Biosciences, ETH Zürich, Computational Science Laboratory, USI Campus, 6900 Lugano, Switzerland.
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Monjardet-Bas V, Bombard S, Chottard JC, Kozelka J. GA and AG sequences of DNA react with cisplatin at comparable rates. Chemistry 2004; 9:4739-45. [PMID: 14566881 DOI: 10.1002/chem.200305085] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The sequence selectivity of the antitumor drug cisplatin (cis-[PtCl(2)(NH(3))(2)] (1)) between the 5'-AG-3' and 5'-GA-3' sites of DNA has been a matter of discussion for more than twenty years. In this work, we compared the reactivity of GA and AG sequences of DNA towards the aquated forms of cisplatin (cis-[PtCl(NH(3))(2)(H(2)O)](+) (2), cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) (3), and cis-[Pt(OH)(NH(3))(2)(H(2)O)](+) (4)) using two sets of experiments. In the first, we investigated a DNA hairpin, whose duplex stem contained a TGAT sequence as the single reactive site, and determined the individual rate constants of platination with 2 and 3 for G and A in acidic solution. The rate constants at 20 degrees C in 0.1M NaClO(4) at pH 4.5+/-0.1 were 0.09(4) M(-1)s(-1) (G) and 0.11(3) M(-1)s(-1) (A) for 2, and 9.6(1) M(-1)s(-1) (G) and 1.7(1) M(-1)s(-1) (A) for 3. These values are similar to those obtained previously for an analogous hairpin that contained a TAGT sequence. The monoadducts formed with 2 by both GA purines are extremely long-lived, partly as a result of the slow hydrolysis of the chloro monoadduct at A, and partly because of the very low chelation rate (1.4 x 10(-5)s(-1) at 20 degrees C) of the aqua monoadduct on the guanine. In the second set of experiments, we incubated pure or enriched samples of 1, 2, 3, or 4 for 18-64 h at 25 degrees C with a 19 base pair (bp) DNA duplex, whose radiolabeled top strand contained one GA and one AG sequence as the only reactive sites. Quantification of the number of GA and AG cross-links afforded a ratio of about two in favor of AG, irrespective of the nature of the leaving ligands. These results disagree with a previous NMR spectroscopy study, and indicate that GA sequences of DNA are substantially more susceptible to attack by cisplatin than previously thought.
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Affiliation(s)
- Véronique Monjardet-Bas
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, CNRS, UMR 8601, 45 rue des Saints-Pères, 75270 Paris, France
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Romerosa A, Bergamini P, Bertolasi V, Canella A, Cattabriga M, Gavioli R, Mañas S, Mantovani N, Pellacani L. Biologically Active Platinum Complexes Containing 8-Thiotheophylline and 8-(Methylthio)theophylline. Inorg Chem 2004; 43:905-13. [PMID: 14753810 DOI: 10.1021/ic034868c] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complexes [Pt(mu-N,S-8-TT)(PPh(3))(2)](2) (1), [Pt(mu-S,N-8-TT)(PTA)(2)](2) (2), [Pt(8-TTH)(terpy)]BF(4) (3), cis-[PtCl(8-MTT)(PPh(3))(2)] (4), cis-[Pt(8-MTT)(2)(PPh(3))(2)] (5), cis-[Pt(8-MTT)(8-TTH)(PPh(3))(2)] (6), cis-[PtCl(8-MTT)(PTA)(2)] (7), cis-[Pt(8-MTT)(2)(PTA)(2)] (8), and trans-[Pt(8-MTT)(2)(py)(2)] (9) (8-TTH(2) = 8-thiotheophylline; 8-MTTH = 8-(methylthio)theophylline; PTA = 1,3,5-triaza-7-phosphaadamantane) are presented and studied by IR and multinuclear ((1)H, (31)P[(1)H]) NMR spectroscopy. The solid-state structure of 4 and 9 has been authenticated by X-ray crystallography. Growth inhibition of the cancer cells T2 and SKOV3 induced by the above new thiopurine platinum complexes has been investigated. The activity shown by complexes 4 and 9 was comparable with cisplatin on T2. Remarkably, 4 and 9 displayed also a valuable activity on cisplatin-resistant SKOV3 cancer cells.
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Affiliation(s)
- A Romerosa
- Area de Química Inorgánica, Facultad de Ciencias Experimentales, Universidad de Almería, 04071 Almería, Spain.
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Baik MH, Friesner RA, Lippard SJ. Theoretical Study of Cisplatin Binding to Purine Bases: Why Does Cisplatin Prefer Guanine over Adenine? J Am Chem Soc 2003; 125:14082-92. [PMID: 14611245 DOI: 10.1021/ja036960d] [Citation(s) in RCA: 225] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thermodynamics and kinetics for the monofunctional binding of the antitumor drug cisplatin, cis-diamminedichloroplatinum(II), to a purine base site of DNA were studied computationally using guanine and adenine as model reactants. A dominating preference for initial attack at the N7-position of guanine is established experimentally, which is a crucial first step for the formation of a 1,2-intrastrand cross-link of adjacent guanine bases that leads to bending and unwinding of DNA. These structural distortions are proposed ultimately to be responsible for the anticancer activity of cisplatin. Utilizing density functional theory in combination with a continuum solvation model, we developed a concept for the initial Pt-N7 bond formation to atomic detail. In good agreement with experiments that suggested DeltaG++ = approximately 23 kcal/mol for the monofunctional platination of guanine, our model gives DeltaG++ = 24.6 kcal/mol for guanine, whereas 30.2 kcal/mol is computed when adenine is used. This result predicts that guanine is 3-4 orders of magnitude more reactive toward cisplatin than adenine. A detailed energy decomposition and molecular orbital analysis was conducted to explain the different barrier heights. Two effects are equally important to give the preference for guanine over adenine: First, the transition state is characterized by a strong hydrogen bond between the ammine-hydrogen of cisplatin and the O=C6 moiety of guanine in addition to a stronger electrostatic interaction between the two reacting fragments. When adenine binds, only a weak hydrogen bond forms between the chloride ligand of cisplatin and the H(2)N-C6 group of adenine. Second, a significantly stronger molecular orbital interaction is identified for guanine compared to adenine. A detailed MO analysis is presented to provide an intuitive view into the different electronic features governing the character of the Pt-N7 bond in platinated purine bases.
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Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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Komeda S, Bombard S, Perrier S, Reedijk J, Kozelka J. Kinetic study of azole-bridged dinuclear platinum(II) complexes reacting with a hairpin-stabilized double-stranded oligonucleotide. J Inorg Biochem 2003; 96:357-66. [PMID: 12888271 DOI: 10.1016/s0162-0134(03)00151-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cytotoxic dinuclear platinum(II) complexes [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-pz)](NO(3))(2) (pz=pyrazolate) (1) and [[cis-Pt(NH(3))(2)](2)(mu-OH)(mu-1,2,3-ta-N1,N2)](NO(3))(2) (1,2,3-ta=1,2,3-triazolate) (2), were allowed to react with the hairpin-stabilized double-stranded oligonucleotide d(TATGGCATT(4)ATGCCATA), to determine the amounts of intrastrand and interstrand DNA adducts. The reaction kinetics was investigated by reversed-phase HPLC, and the resulting products were analyzed using mass spectroscopy combined with enzymatic digestion, and Maxam-Gilbert sequencing. The reaction of 1 results in the formation of the 1,2-intrastrand d(GG) adduct as the major final product. The two most abundant products of 2 were identified as isomeric 1,2-intrastrand d(GG) adducts differing probably in platinum coordination to the triazole ring. No GG-interstrand crosslinks were detected with either compound. d(GGC)-d(GCC) sequences of DNA do thus not appear to represent significant targets for forming interstrand crosslinks with either 1 or 2.
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Affiliation(s)
- Seiji Komeda
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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