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Margiotta N, Petruzzella E, Platts JA, Mutter ST, Deeth RJ, Ranaldo R, Papadia P, Marzilli PA, Marzilli LG, Hoeschele JD, Natile G. DNA fragment conformations in adducts with Kiteplatin. Dalton Trans 2015; 44:3544-56. [DOI: 10.1039/c4dt01796j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anticancer-active platinum complex with cis-1,4-diaminocyclohexane has proved to be very valuable in detecting multiple conformers in adducts with oligonucleotides.
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Affiliation(s)
- Nicola Margiotta
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
| | | | | | | | | | - Rosa Ranaldo
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
- Department of Chemistry
| | - Paride Papadia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali
- Università del Salento
- 73100 Lecce
- Italy
| | | | | | | | - Giovanni Natile
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
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Saad JS, Marzilli PA, Intini FP, Natile G, Marzilli LG. Single-stranded oligonucleotide adducts formed by Pt complexes favoring left-handed base canting: steric effect of flanking residues and relevance to DNA adducts formed by Pt anticancer drugs. Inorg Chem 2011; 50:8608-20. [PMID: 21819051 DOI: 10.1021/ic2011716] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Platinum anticancer drug binding to DNA creates large distortions in the cross-link (G*G*) and the adjacent XG* base pair (bp) steps (G* = N7-platinated G). These distortions, which are responsible for anticancer activity, depend on features of the duplex (e.g., base pairing) and of the cross-link moiety (e.g., the position and canting of the G* bases). The duplex structure stabilizes the head-to-head (HH) over the head-to-tail (HT) orientation and right-handed (R) over left-handed (L) canting of the G* bases. To provide fundamental chemical information relevant to the assessment of such duplex effects, we examine (S,R,R,S)-BipPt(oligo) adducts (Bip = 2,2'-bipiperidine with S,R,R,S chiral centers at the N, C, C, and N chelate ring atoms, respectively; oligo = d(G*pG*) with 3'- and/or 5'-substituents). The moderately bulky (S,R,R,S)-Bip ligand favors L canting and slows rotation about the Pt-G* bonds, and the (S,R,R,S)-BipPt(oligo) models provide more useful data than do dynamic models derived from active Pt drugs. All 5'-substituents in (S,R,R,S)-BipPt(oligo) adducts favor the normal HH conformer (∼97%) by destabilizing the HT conformer through clashes with the 3'-G* residue rather than through favorable H-bonding interactions with the carrier ligand in the HH conformer. For all (S,R,R,S)-BipPt(oligo) adducts, the S pucker of the 5'-X residue is retained. For these adducts, a 5'-substituent had only modest effects on the degree of L canting for the (S,R,R,S)-BipPt(oligo) HH conformer. This small flanking 5'-substituent effect on an L-canted HH conformer contrasts with the significant decrease in the degree of R canting previously observed for flanking 5'-substituents in the R-canted (R,S,S,R)-BipPt(oligo) analogues. The present data support our earlier hypothesis that the distortion distinctive to the XG* bp step (S to N pucker change and movement of the X residue) is required for normal stacking and X·X' WC H bonding and to prevent XG* residue clashes.
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Affiliation(s)
- Jamil S Saad
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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Maheshwari V, Marzilli PA, Marzilli LG. Investigation Relevant to the Conformation of the 17-Membered Pt(d(GpG)) Macrocyclic Ring Formed by Pt Anticancer Drugs with DNA: Pt Complexes with a Goldilocks Carrier Ligand. Inorg Chem 2011; 50:6626-36. [DOI: 10.1021/ic200512m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vidhi Maheshwari
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Saad JS, Natile G, Marzilli LG. Origins of the Distortions in the Base Pair Step Adjacent to Platinum Anticancer Drug−DNA Adducts. Fundamental NMR Solution Studies Utilizing Right-Handed Cross-Link Models Having 5′- and 3′-Flanking Residues. J Am Chem Soc 2009; 131:12314-24. [DOI: 10.1021/ja903787m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jamil S. Saad
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Giovanni Natile
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Luigi G. Marzilli
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
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Maheshwari V, Marzilli PA, Marzilli LG. Neglected Bidentate sp2 N-Donor Carrier Ligands with Triazine Nitrogen Lone Pairs: Platinum Complexes Retromodeling Cisplatin Guanine Nucleobase Adducts. Inorg Chem 2008; 47:9303-13. [DOI: 10.1021/ic800836t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vidhi Maheshwari
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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Mantri Y, Lippard SJ, Baik MH. Bifunctional binding of cisplatin to DNA: why does cisplatin form 1,2-intrastrand cross-links with ag but not with GA? J Am Chem Soc 2007; 129:5023-30. [PMID: 17402732 PMCID: PMC2495024 DOI: 10.1021/ja067631z] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bifunctional binding of the anticancer drug cisplatin to two adjacent nucleobases in DNA is modeled using density functional theory. Previous experimental studies revealed that cisplatin binding to adjacent guanine and adenine is sensitive to nucleobase sequence. Whereas AG 1,2-intrastrand cross-links are commonly observed, the analogous GA adducts are not known. This study focuses on understanding this directional preference by constructing a full reaction profile using quantum chemical simulation methods. Monofunctional and bifunctional cisplatin adducts were generated, and the transition states that connect them were located for the dinucleotides d(pApG) and d(pGpA), assuming that initial platination takes place at the guanine site. Our computer simulations reveal a significant kinetic preference for formation of the AG over the GA adduct. The activation free energies of approximately 23 kcal/mol for AG and approximately 32 kcal/mol for GA suggest that bifunctional closure is approximately 6 orders of magnitude faster for AG than for GA. A strong hydrogen bond between one of the ammine ligands of cisplatin and the 5' phosphate group of the DNA backbone is responsible for the stabilization of the transition state that affords the AG adduct. This interaction is absent in the transition state that leads to the GA adduct because the right-handed helix of the DNA backbone places the phosphate out of reach for the ammine ligand. We found only an insignificant thermodynamic difference between AG and GA adducts and conclude that the preference of AG over GA binding is largely under kinetic control. The puckering of the deoxyribose ring plays an important role in determining the energetics of the bifunctional platination products. Whereas the 3'-nucleoside remains in the native C2'-endo/C3'-exo form of B-DNA, the deoxyribose of the 5'-nucleoside always adopts the C2'-exo/C3'-endo puckering in our simulations. A detailed analysis of the energies and structures of the bifunctional adducts revealed that the observed sugar puckering patterns are necessary for platinum to bind in a relaxed coordination geometry.
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Affiliation(s)
- Yogita Mantri
- Department of Chemistry and School of Informatics, Indiana University, Bloomington, Indiana 47405, USA
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Swiatek J. REVIEW: INTERACTIONS OF METAL IONS WITH NUCLEIC ACIDS AND THEIR SUBUNITS. AN ELECTROCHEMICAL APPROACH. J COORD CHEM 2006. [DOI: 10.1080/00958979408024278] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jolanta Swiatek
- a Department of Basic Medical Sciences , Medical Academy of Wroclaw , Kochanowskiego, 14, 51-601, Wroclaw , Poland
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Natile G, Marzilli LG. Non-covalent interactions in adducts of platinum drugs with nucleobases in nucleotides and DNA as revealed by using chiral substrates. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2005.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Saad JS, Scarcia T, Shinozuka K, Natile G, Marzilli LG. Modification of second-sphere communication, leading to an unusually high abundance of the head-to-head conformer of cisplatin cross-link retro models. Inorg Chem 2002; 41:546-57. [PMID: 11825082 DOI: 10.1021/ic010758z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid atropisomerization of cisplatin-DNA cross-link models, cis-PtA(2)G(2) (A(2) = two amines or a diamine, G = guanine derivative, bold font indicating a guanine not linked to another guanine), makes their NMR spectra uninformative. The conformers [two head-to-tail (DeltaHT and LambdaHT) conformers, one head-to-head (HH) conformer] are detected in (CCC)PtG(2) retro models (CCC = chirality-controlling chelates designed to reduce rotation around the G N7 to Pt bond by destabilizing the transition state). Clear trends are found with four CCC ligands, 2,2'-bipiperidine (Bip) and N,N'-dimethyl-2,3-diaminobutane (each with S,R,R,S and R,S,S,R configurations at the chelate ring N, C, C, and N atoms, respectively). S,R,R,S ligands favor left-handed G base canting and the LambdaHT form; R,S,S,R ligands favor right-handed canting and the DeltaHT form. The HH conformer is normally negligible unless G = 5'-GMP. However, understanding this 5'-phosphate effect is complicated by possible interligand interactions of the 5'-phosphate with the N1H of the cis-5'-GMP and a CCC NH; these interactions are referred to as second-sphere (SSC) and first-to-second-sphere (FSC) communication, respectively. We now investigate the four (CCC)PtG(2) models with 1-Me-5'-GMP, a G lacking the N1H needed for SSC. The phosphate location makes FSC possible in the major but not the minor HT form. The major form should increase from pH 3 to pH 7 because the phosphate is deprotonated at pH 7. However, the major DeltaHT form for the R,S,S,R pair did not change in abundance, and the major LambdaHT form for the S,R,R,S pair actually decreased. Thus, FSC is weak. At pH approximately 7 the HH conformer of the S,R,R,S pair had an abundance (40-44%) higher than that in any reported cis-PtA(2)G(2) adduct. FSC involving one 1-Me-5'-GMP could play a role. The high HH abundance and use of a pH jump experiment with (S,R,R,S)-BipPt(1-Me-5'-GMP)(2) allowed us to obtain the first deconvoluted CD spectrum for a cis-PtA(2)G(2) HH conformer. The CD features for the HH conformer are much weaker than for the HT conformers. Our findings are best interpreted to indicate that FSC is not important in aqueous solution, especially for the HT form. Weak FSC is consistent with recent models of the cross-link in duplexes. In contrast, crystals of fluxional models often reveal FSC, but not the more important SSC. SSC was unrecognized until our retro model studies, and the new results reinforce the value of studying retro models for identifying interactions in solution.
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Affiliation(s)
- Jamil S Saad
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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Malina J, Hofr C, Maresca L, Natile G, Brabec V. DNA interactions of antitumor cisplatin analogs containing enantiomeric amine ligands. Biophys J 2000; 78:2008-21. [PMID: 10733979 PMCID: PMC1300793 DOI: 10.1016/s0006-3495(00)76748-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Modifications of natural DNA and synthetic oligodeoxyribonucleotide duplexes in a cell-free medium by analogs of antitumor cisplatin containing enantiomeric amine ligands, such as cis-[PtCl(2)(RR-DAB)] and cis-[PtCl(2)(SS-DAB)] (DAB = 2,3-diaminobutane), were studied by various methods of molecular biophysics and biophysical chemistry. These methods include DNA binding studies by pulse polarography and atomic absorption spectrophotometry, mapping of DNA adducts using transcription assay, interstrand cross-linking assay using gel electrophoresis under denaturing conditions, differential scanning calorimetry, chemical probing, and bending and unwinding studies of the duplexes containing single, site-specific cross-link. The major differences resulting from the modification of DNA by the two enantiomers are the thermodynamical destabilization and conformational distortions induced in DNA by the 1,2-d(GpG) intrastrand cross-link. It has been suggested that these differences are associated with a different biological activity of the two enantiomers observed previously. In addition, the results of the present work are also consistent with the view that formation of hydrogen bonds between the carbonyl oxygen of the guanine residues and the "quasi equatorial" hydrogen of the cis amine in the 1, 2-d(GpG) intrastrand cross-link plays an important role in determining the character of the distortion induced in DNA by this lesion.
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Affiliation(s)
- J Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Ano SO, Intini FP, Natile G, Marzilli LG. Retro Models of Pt Anticancer Drug DNA Adducts: Chirality-Controlling Chelate Ligand Restriction of Guanine Dynamic Motion in (2,2'-Bipiperidine)PtG(2) Complexes (G = Guanine Derivative). Inorg Chem 1999; 38:2989-2999. [PMID: 11671050 DOI: 10.1021/ic981409g] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Features of cisplatin-type anticancer drug adducts with nucleic acids and their constituents are clouded because they exist as a fluxional mixture of conformers. Retro-model adducts containing the specially designed chiral diamine ligand, Bip = 2,2'-bipiperidine, are dramatically less fluxional. Conformers of BipPtG(2) adducts with R,S,S,R and S,R,R,S asymmetric centers at the N, C, C, and N Bip chelate ring atoms and G = 5'-GMP, 5'-dGMP, 3'-GMP, or 9-ethylguanine are amenable to separate characterization. All possible BipPtG(2) atropisomers (one head-to-head (HH) and Delta and Lambda head-to-tail (HT) atropisomers) were observed by NMR spectroscopy. At equilibrium at low pH, one HT atropisomer dominates. CD spectra, G H8 chemical shifts, and low-pH equilibria of BipPtG(2) and Me(2)()DABPtG(2) (Me(2)()DAB = N,N '-dimethyl-2,3-diaminobutane) are similar when the chelate ring atoms have the same stereochemistries; thus, Bip and Me(2)()DAB are termed chirality-controlling chelates (CCC) since these ligands dictate the absolute conformation of the major HT rotamer. In each case, the HT conformer that cannot form G O6-NH(CCC) hydrogen bonds was dominant, and the G H8 chemical shift indicated that this conformer had less tilted bases, allowing favorable base-base dipole-dipole interactions. For both the R,S,S,R and S,R,R,S Bip chiralities of the BipPt(3'-GMP)(2) complexes, the percentage of DeltaHT rotamer increased near pH 7, a probable consequence of phosphate-cis-G hydrogen bonds accompanied by favorable dipole interactions of less tilted bases. For the 5'-GMP complexes, these factors favor the LambdaHT rotamer near pH 7. When G has a 5'-phosphate group, rotamer distribution is also influenced by phosphate-NH(Bip) hydrogen bonds. At high pH, the nature and/or strength of interactions such as G dipole-G dipole interactions and G O6-NH(Bip) and phosphate-cis-G hydrogen bonding are altered by G N(1)H deprotonation. The features of the complexes at high pH can be largely explained as arising from the net result of these interactions. This information from retro models with a CCC ligand lays the foundation for understanding and evaluating the properties of the highly dynamic adducts of anticancer drugs.
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Affiliation(s)
- Susan O. Ano
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università degli Studi di Bari, 70125 Bari, Italy
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Marzilli LG, Intini FP, Kiser D, Wong HC, Ano SO, Marzilli PA, Natile G. Chirality-Controlling Chelate (CCC) Ligands in Analogues of Platinum Anticancer Agents. Influence of N9 Substituents of Guanine Derivatives (G) on the Distribution of Chiral Conformers of (CCC)PtG(2) with CCC = N,N'-Dimethyl-2,3-diaminobutane. Inorg Chem 1998; 37:6898-6905. [PMID: 11670827 DOI: 10.1021/ic980843f] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chirality-controlling chelate (CCC) ligands are a class of chiral diamine ligands with one or two chiral secondary amine ligating groups. Analogues of platinum anticancer agents containing CCC ligands exhibit unusual steric and dynamic features. In this study NMR and CD methods were used to evaluate the influence of the N9 substituent in guanine derivatives (G) on conformer distribution in one class of (CCC)PtG(2)() complexes. We employed the CCC ligand, N,N'-dimethyl-2,3-diaminobutane [Me(2)()DAB with S,R,R,S or R,S,S,R configurations at the four asymmetric centers, N, C, C, and N]. For each Me(2)()DABPtG(2) complex, the presence of four G H8 signals demonstrated formation of all three possible atropisomers: DeltaHT (head-to-tail), LambdaHT, and HH (head-to-head). Different G ligands (5'-GMP, 3'-GMP, 1-MeGuo, Guo, or 9-EtG) were chosen to assess the effect of the N9 substituent on the relative stability and spectral properties of the atropisomers. The conformations of the atropisomers of Me(2)()DABPtG(2) were determined from CD spectra and from NOE cross-peaks (assigned via COSY spectra) between G H8 signals and those for the Me(2)()DAB protons. Regardless of the N9 substituent, the major form was HT. However, this form had the opposite chirality, LambdaHT and DeltaHT, and base tilt direction, left- and right-handed, respectively, for the S,R,R,S and R,S,S,R configurations of the Me(2)()DAB ligand. Thus, the chirality of the CCCligand, not hydrogen bonding, is the most important determinant of conformation. For each Me(2)()DABPtG(2) complex, the tilt direction of all three atropisomers is the same and, except for 5'-GMP, the order of abundance was major HT > minor HT > HH. For 5'-GMP, the HH atropisomer was three times as abundant as the minor HT species, suggesting that phosphate-NH(Me(2)()DAB) hydrogen bonds could be present since such bonding is possible only for the 5'-GMP derivatives. However, if such phosphate-NH hydrogen bonds exist, they are weak since the percentage of the major HT form of 5'-GMP complexes is similar and indeed can be smaller compared to this percentage for complexes with other G's. The CD spectra of all (S,R,R,S)-Me(2)()DABPtG(2) complexes were similar and opposite to those of all (R,S,S,R)-Me(2)()DABPtG(2) complexes, indicating the CD signature is characteristic of the dominant HT conformer, which has a chirality dictated by the chirality of the CCC ligand and not the N9 substituent.
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Affiliation(s)
- Luigi G. Marzilli
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università degli Studi di Bari, 70125 Bari, Italy
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Hambley TW, Ling ECH, Messerle BA. Combined NMR and Molecular Mechanics Study of the Isomers Formed in the Reaction of Dichloro(1,4-diazacycloheptane)platinum(II) with the Dinucleotide d(GpG). Inorg Chem 1996. [DOI: 10.1021/ic951489d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trevor W. Hambley
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Edwina C. H. Ling
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
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Garoufis A, Louloudi M, Kasselouri S, Hatiris J, Hadjiliadis N. Ternary complexes of copper(II) containing inosine (Ino), guanosine (Guo) and the dipeptides, GLY-GLY, GLY-l-ALA, GLY-l-VAL and GLY-l-LEU. Polyhedron 1995. [DOI: 10.1016/0277-5387(94)00381-n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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McCarthy SL, Hinde RJ, Miller KJ, Anderson JS, Basch H, Krauss M. Theoretical studies of cis-Pt(II)-diammine binding to duplex DNA. Biopolymers 1990; 29:823-36. [PMID: 2383646 DOI: 10.1002/bip.360290416] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding of cis-Pt(II) diammine (cis-DP) to double-stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2')-endo or C(1')-exo (S), to the type C(3')-endo or C(2')-exo (N), with intermediate types near O(1')-endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3'-TpG*pG*p-5'), with the complexed strand exhibiting, (3')-S*-N*-S-(5') alternation, while the complementary strand shows either (3')-S*-N*-S-(5') or (3')-S*-N*-O-(5') alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3') end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis-Pt(II)-diammines to adjacent N7(G) in double-stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton-proton distances are reported to assist in the experimental determination of conformations.
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Affiliation(s)
- S L McCarthy
- Department of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180
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trans-ternary complexes of Pd(II) with nucleosides and dipeptides. Models for trans-DDP-DNA-protein crosslinks. Inorganica Chim Acta 1989. [DOI: 10.1016/s0020-1693(00)80816-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Umapathy P. The chemical and biochemical consequences of the binding of the antitumour drug cisplatin and other platinum group metal complexes to DNA. Coord Chem Rev 1989. [DOI: 10.1016/0010-8545(89)80025-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Johnson NP, Butour JL, Villani G, Wimmer FL, Defais M, Pierson V, Brabec V. Metal Antitumor Compounds: The Mechanism of Action of Platinum Complexes. RUTHENIUM AND OTHER NON-PLATINUM METAL COMPLEXES IN CANCER CHEMOTHERAPY 1989. [DOI: 10.1007/978-3-642-74760-1_1] [Citation(s) in RCA: 128] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lepre CA, Strothkamp KG, Lippard SJ. Synthesis and 1H NMR spectroscopic characterization of trans-[Pt(NH3)2[d(ApGpGpCpCpT)-N7-A(1),N7-G(3)]]. Biochemistry 1987; 26:5651-7. [PMID: 3676275 DOI: 10.1021/bi00392a011] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The reaction of trans-[Pt(NH3)2Cl2] with the sodium salt of [d(ApGpGpCpCpT)]2 in aqueous solution at 37 degrees C was monitored by reversed-phase high-performance liquid chromatography and UV spectroscopy. Two intermediates, most likely monofunctional adducts, were observed, which subsequently formed one predominant single-stranded product, as well as several polymeric species proposed to be interstrand cross-linked products. The single-stranded adduct was structurally characterized by 1H NMR spectroscopy. From the pH dependence of the chemical shifts, two-dimensional homonuclear chemical shift correlation (COSY) spectroscopy, and one- and two-dimensional nuclear Overhauser effect (NOESY) experiments, the platinum(II) moiety was found to be coordinated to the N7 positions of adenine(1) and guanine(3), with the intervening guanine(2) base destacked from its neighboring residues. This intrastrand 1,3 adduct induces changes in the backbone torsion angles and causes the deoxyribose ring of adenine(1) to switch from a C2'-endo to a predominantly C3'-endo conformation. The other deoxyribose rings retain B DNA type conformations. The structure of trans-[Pt(NH3)2[d(ApGpGpCpCpT)-N7-A(1),N7-G(3)]] differs from those previously reported for cis-DDP 1,2- and 1,3-intrastrand oligonucleotide adducts but is consistent with the structures of trans-DDP 1,3-intrastrand adducts of two previously reported trinucleotides.
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Affiliation(s)
- C A Lepre
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139
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22
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Garoufis A, Haran R, Pasdeloup M, Laussac JP, Hadjiliadis N. Interaction of cis-Pt(ino)2Cl2 with amino acids. J Inorg Biochem 1987; 31:65-79. [PMID: 3694197 DOI: 10.1016/0162-0134(87)85006-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The reactions of cis-Pt(ino)2Cl2 with the amino acids Gly, L-Ala, L-Val, L-Ileu, L-Phe and L-Pro were studied in methanolic solutions. The (1:1) adducts of the formulas cis-[Pt(ino)2(am-ac)]Cl were isolated from these reactions in the solid state, which in turn produce the cis-[Pt(ino)2(am-acH)Cl]Cl complexes, by treating the former with equivalent amounts of HCl, in aqueous solutions. The complexes were characterized with elemental analysis, conductivity measurements, IR, 1H NMR, and 13C NMR spectra. The results show that the purine ring of inosine interacts with the aliphatic side chain of the amino acids. The platination increases the percentage of the C3'-endo-anti conformation of the sugar part of inosine.
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Affiliation(s)
- A Garoufis
- Department of Chemistry, University of Ioannina, Greece
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23
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Okamoto K, Benham V, Theophanides T. FT-IR spectroscopic evidence of sugar ring conformational changes in GpC and CpG on platination and intercalation. Inorganica Chim Acta 1987. [DOI: 10.1016/s0020-1693(00)81300-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Okamoto K, Behnam V, Gauthier JY, Hanessian S, Theophanides T. An FT-IR and 1H NMR spectral study of sugar ring conformations in guanosine and in several platinum(II) complexes. Inorganica Chim Acta 1986. [DOI: 10.1016/s0020-1693(00)81303-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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FT-IR and 1H NMR spectroscopic studies of C2′- endo, C3′-endo sugar ring conformations in 5′-GMP and 3′-GMP nucleotides and their platinum complexes. Inorganica Chim Acta 1986. [DOI: 10.1016/s0020-1693(00)81304-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Okamoto K, Behnam V, Theophanides T. FT-IR and 1H NMR spectroscopic evidence of sugar ring conformational change in NH4GpG on complexation to form cis-[Pt(NH3)2(GpG)]+. Inorganica Chim Acta 1985. [DOI: 10.1016/s0020-1693(00)81287-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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den Hartog JH, Altona C, van Boom JH, van der Marel GA, Haasnoot CA, Reedijk J. cis-diamminedichloroplatinum(II) induced distortion of a single and double stranded deoxydecanucleosidenonaphosphate studied by nuclear magnetic resonance. J Biomol Struct Dyn 1985; 2:1137-55. [PMID: 3916945 DOI: 10.1080/07391102.1985.10507629] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The structural distortion of a single- and a double-stranded decadeoxynucleotide upon binding of cis-PtCl2(NH3)2 was studied by 1H-NMR. After selective platination of d(T-C-T-C-G-G-T-C-T-C) (I) at the central d(-GpG-) site (resulting in I-Pt), several non-exchangeable base protons as well as H1', H2', H2" and H3' protons could be assigned by means of conventional NMR double-resonance techniques. Addition of the complementary decamer strand to I and I-Pt yielded the double-stranded III and III-Pt, respectively. All non-exchangeable base, H1', and most of the H2' and H2" protons in the two double stranded compounds could be assigned using 2D-chemical shift correlation (COSY) and nuclear Overhauser enhancement (NOESY) techniques. The double stranded compound III appears to adopt a B-DNA like structure. Comparison of NOEs and proton-proton coupling constants in the d(-GpG-).cisPt part in I-Pt and III-Pt reveals that their structure displays large similarity. Significant chemical shift changes (i.e. larger than 0.1 ppm) between III and III-Pt are restricted to the central four base pairs. It follows that the outer three base pairs, located on either side of the central four base pairs in III-Pt are likely to adopt a regular B-DNA type helix. The observed large upfield and downfield chemical shifts in the d(-CpGpG-) part of III with respect to III-Pt can be rationalized by describing the distortion of the double helix as a kink. A discussion of the observed physical effects upon platination of a double-stranded oligonucleotide is presented.
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Affiliation(s)
- J H den Hartog
- Department of Chemistry, Gorlaeus Laboratory, State University Leiden, The Netherlands
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28
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den Hartog JH, Altona C, van der Marel GA, Reedijk J. A 1H and 31P NMR study of cis-Pt(NH3)2[d(CpGpG)-N7(2),N7(3)]. The influence of a 5'-terminal cytosine, on the structure of the cis-Pt(NH3)2[d(GpG)-N7,N7] intrastrand cross-link. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 147:371-9. [PMID: 2982616 DOI: 10.1111/j.1432-1033.1985.tb08760.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proton NMR studies at 300 MHz and 500 MHz have been carried out on the trinucleoside bisphosphate d(CpGpG) and on cis-Pt(NH3)2[d(CpGpG)-N7(2),N7(3)] [abbreviated as d(CpGpGp) . cisPt]. For the Pt adduct, 13C and 31P NMR was also used for characterizing the oligonucleotide. d(CpGpG) appears to revert to a B-DNA-type single helix at lower temperatures. The relatively small concentration dependence of the proton chemical shifts, in comparison with shifts due to intramolecular stacking effects, indicates that the compound is essentially single-stranded. In d(CpGpGp) . cisPt, the first nucleoside, C(1), stacks well on top of the second, G(2), despite the N conformation of the G(2) sugar ring. The platinated GpG part in this trimer adopts largely the same structure as in cis-Pt(NH3)2[d(GpGpG)-N7(1),N7(2)] [den Hartog, J. H. J., et al. (1982) Nucleic Acids Res. 10, 4715-4730]. Main differences however, are changes in H8 chemical shifts and a 0.6-ppm downfield shift of the third nucleotide phosphorus, P(3), in d(CpGpGp) . cisPt with respect to P(2) in d(GpG) . cisPt. The latter shift change is likely to be induced by a structural alteration, caused by stacking of C(1) on top of G(2). Also, the large chemical shift differences between the two H8 protons in d(NpGpG) . cisPt fragments is discussed; the deviation from a mirror symmetry of the two guanine bases seems to be the main origin of this effect. The chemical shift changes, observed in the proton and phosphorus NMR chemical shift temperature and chemical shift pH profiles have been explained in terms of stack-destack equilibria changes.
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