1
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Farrokhpour H, Mokhtari N. Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li +: NBO, QTAIM, and computational spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123896. [PMID: 38266601 DOI: 10.1016/j.saa.2024.123896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine-thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair's site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.
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Affiliation(s)
- Hossein Farrokhpour
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | - Nikoo Mokhtari
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
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2
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Greco R, García-Lainez G, Oliver-Meseguer J, Marini C, Domínguez I, López-Haro M, Hernández-Garrido JC, Cerón-Carrasco JP, Andreu I, Leyva-Pérez A. Cytotoxic sub-nanometer aqueous platinum clusters as potential antitumoral agents. NANOSCALE ADVANCES 2022; 4:5281-5289. [PMID: 36540110 PMCID: PMC9724608 DOI: 10.1039/d2na00550f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/09/2022] [Indexed: 06/17/2023]
Abstract
Ligand-free sub-nanometer metal clusters (MCs) of Pt, Ir, Rh, Au and Cu, are prepared here in neat water and used as extremely active (nM) antitumoral agents for HeLa and A2870 cells. The preparation just consists of adding the biocompatible polymer ethylene-vinyl alcohol (EVOH) to an aqueous solution of the corresponding metal salt, to give liters of a MC solution after filtration of the polymer. Since the MC solution is composed of just neat metal atoms and water, the intrinsic antitumoral activity of the different sub-nanometer metal clusters can now fairly be evaluated. Pt clusters show an IC50 of 0.48 μM for HeLa and A2870 cancer cells, 23 times higher than that of cisplatin and 1000 times higher than that of Pt NPs, and this extremely high cytotoxicity also occurs for cisplatin-resistant (A2870 cis) cells, with a resistance factor of 1.4 (IC50 = 0.68 μM). Rh and Ir clusters showed an IC50 ∼ 1 μM. Combined experimental and computational studies support an enhanced internalization and cytotoxic activation.
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Affiliation(s)
- Rossella Greco
- Instituto de Tecnología Química (UPV-CSIC) Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas Avda. de los Naranjos s/n 46022 Valencia Spain
| | - Guillermo García-Lainez
- Instituto de Investigación Sanitaria (IIS) La Fe, Unidad Mixta de Investigación UPV/IIS La Fe, Hospital Universitari i Politècnic La Fe Avenida de Fernando Abril Martorell 106 46026 Valencia Spain
| | - Judit Oliver-Meseguer
- Instituto de Tecnología Química (UPV-CSIC) Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas Avda. de los Naranjos s/n 46022 Valencia Spain
| | - Carlo Marini
- CELLS-ALBA Synchrotron E-08290 Cerdanyola del Vallès Barcelona Spain
| | - Irene Domínguez
- Department of Chemistry and Physics, University of Almeria, Agrifood Campus of International Excellence ceiA3 04120 Almeria Spain
| | - Miguel López-Haro
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, Campus Río San Pedro 11510 Puerto Real Cádiz Spain
| | - Juan Carlos Hernández-Garrido
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica, Facultad de Ciencias, Universidad de Cádiz, Campus Río San Pedro 11510 Puerto Real Cádiz Spain
| | - José Pedro Cerón-Carrasco
- Centro Universitario de la Defensa, Academia General del Aire. Universidad Politécnica de Cartagena. C/ Coronel López Peña S/N Santiago de La Ribera, 30720 Murcia Spain
| | - Inmaculada Andreu
- Instituto de Investigación Sanitaria (IIS) La Fe, Unidad Mixta de Investigación UPV/IIS La Fe, Hospital Universitari i Politècnic La Fe Avenida de Fernando Abril Martorell 106 46026 Valencia Spain
- Departamento de Química, Universitat Politècnica de València Camino de Vera s/n 46022 València Spain
| | - Antonio Leyva-Pérez
- Instituto de Tecnología Química (UPV-CSIC) Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas Avda. de los Naranjos s/n 46022 Valencia Spain
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3
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Leitão MIPS, Gonzalez C, Francescato G, Filipiak Z, Petronilho A. On the reactivity of mRNA Cap0: C-H oxidative addition of 7-methylguanosine to Pt 0 and base pairing studies. Chem Commun (Camb) 2020; 56:13365-13368. [PMID: 33030477 DOI: 10.1039/d0cc06075e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
7-Methylguanosine, whose lability to form an ylide/NHC has been known for decades, reacts with [Pt(PPh3)4] via C-H oxidative addition to yield a hydrido-PtII carbene complex. 1H NMR studies on Watson-Crick base-pairs showed no significant effect of metallation.
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Affiliation(s)
- Maria Inês P S Leitão
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Carmen Gonzalez
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Giulia Francescato
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Zuzanna Filipiak
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Ana Petronilho
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
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Jacquemin D, Zúñiga J, Requena A, Céron-Carrasco JP. Assessing the importance of proton transfer reactions in DNA. Acc Chem Res 2014; 47:2467-74. [PMID: 24849375 DOI: 10.1021/ar500148c] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.
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Affiliation(s)
- Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, Nantes 44322 Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, Paris 75005 Cedex 5, France
| | - José Zúñiga
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - José Pedro Céron-Carrasco
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
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Chval Z, Kabeláč M, Burda JV. Mechanism of the cis-[Pt(1R,2R-DACH)(H2O)2]2+ intrastrand binding to the double-stranded (pGpG)·(CpC) dinucleotide in aqueous solution: a computational DFT study. Inorg Chem 2013; 52:5801-13. [PMID: 23656523 DOI: 10.1021/ic302654s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A mechanism of the intrastrand 1,2-cross-link formation between the double-stranded pGpG·CpC dinucleotide (ds(pGpG)) and fully aquated oxaliplatin cis-[Pt(DACH)(H2O)2](2+) (DACH = cyclohexane-1R,2R-diamine) is presented. All structures of the reaction pathways including the transition states (TSs) were fully optimized in water solvent using DFT methodology with dispersion corrections. Both 5' → 3' and 3' → 5' binding directions were considered. In the first step there is a slight kinetic preference for 5'-guanine (5'G) monoadduct formation with an activation Gibbs free energy of 18.7 kcal/mol since the N7 center of the 5'G base is fully exposed to the solvent. On the other hand, the N7 atom of 3'-guanine (3'G) is sterically shielded by 5'G. The lowest energy path for formation of the 3'G monoadduct with an activation barrier of 19.3 kcal/mol is connected with a disruption of the 'DNA-like' structure of ds(pGpG). Monoadduct formation is the rate-determining process. The second step, chelate formation, is kinetically preferred in the 3' → 5' direction. The whole process of the platination is exergonic by up to -18.8 kcal/mol. Structural changes of ds(pGpG), charge transfer effects, and the influence of platination on the G·C base pair interaction strengths are also discussed in detail.
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Affiliation(s)
- Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, 370 11 České Budějovice, Czech Republic.
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6
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Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study. J Mol Model 2012; 19:4669-80. [DOI: 10.1007/s00894-012-1442-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 04/18/2012] [Indexed: 11/26/2022]
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7
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Cerón-Carrasco JP, Requena A, Jacquemin D. Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1188-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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8
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Michera L, Nekadová M, Burda JV. Reactions of cisplatin and glycine in solution with constant pH: a computational study. Phys Chem Chem Phys 2012; 14:12571-9. [DOI: 10.1039/c2cp41016h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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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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10
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Cerón-Carrasco JP, Jacquemin D. Influence of Mg2+ on the Guanine-Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer. Chemphyschem 2011; 12:2615-23. [DOI: 10.1002/cphc.201100264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/28/2011] [Indexed: 01/01/2023]
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11
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Xing D, Tan X, Jiang X, Wang B. Deprotonation studies of Cu+–guanine and Cu2+–guanine complexes by theoretical investigation. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Zimmermann T, Burda JV. Cisplatin interaction with amino acids cysteine and methionine from gas phase to solutions with constant pH. Interdiscip Sci 2010; 2:98-114. [PMID: 20640800 DOI: 10.1007/s12539-010-0094-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 10/19/2022]
Abstract
This work is focused on the computational studies of reactions of hydrated forms of cisplatin with sulphur-containing amino acids cysteine and methionine. First, the appropriate model for solvation of the examined complexes was searched for. The suggested procedure employs the B3LYP density functional, 6-311++G(2df,2pd) basis set with Stuttgart-Dresden pseudopotentials on heavy atoms, the D-PCM solvation model and the UAKS cavity which uses more realistic NPA partial charges instead of formal partial charges for platinum ligands. In the second part this model is applied to the evaluation of the Legendre transformed reaction Gibbs free energy of cisplatin with cysteine and methionine in solution at constant pH.
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Affiliation(s)
- Tomás Zimmermann
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, Czech Republic
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13
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Dans PD, Coitiño EL. Density Functional Theory Characterization and Descriptive Analysis of Cisplatin and Related Compounds. J Chem Inf Model 2009; 49:1407-19. [DOI: 10.1021/ci800421w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pablo D. Dans
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Iguá 4225, 11400 Montevideo, Uruguay
| | - E. Laura Coitiño
- Laboratorio de Química Teórica y Computacional (LQTC), Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Iguá 4225, 11400 Montevideo, Uruguay
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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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15
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Wu Y, Sa R, Li Q, Wei Y, Wu K. Theoretical studies on the bonding of Cd2+ to adenine and thymine: Tautomeric equilibrium and metalation in base pairing. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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16
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Chval Z, Sip M, Burda JV. The trans effect in square-planar platinum(II) complexes-A density functional study. J Comput Chem 2008; 29:2370-81. [DOI: 10.1002/jcc.20980] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Lippert B. Ligand-pKaShifts through Metals: Potential Relevance to Ribozyme Chemistry. Chem Biodivers 2008; 5:1455-1474. [DOI: 10.1002/cbdv.200890135] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Xing D, Tan X, Chen X, Bu Y. Theoretical Study on the Gas-Phase Acidity of Multiple Sites of Cu+−Adenine and Cu2+−Adenine Complexes. J Phys Chem A 2008; 112:7418-25. [PMID: 18646734 DOI: 10.1021/jp800256v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dianxiang Xing
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and School of Chemical Engineering, Shandong Institute of Light Industry, Jinan 250353, P. R. China
| | - Xuejie Tan
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and School of Chemical Engineering, Shandong Institute of Light Industry, Jinan 250353, P. R. China
| | - Xiaohua Chen
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and School of Chemical Engineering, Shandong Institute of Light Industry, Jinan 250353, P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China, and School of Chemical Engineering, Shandong Institute of Light Industry, Jinan 250353, P. R. China
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19
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Dans PD, Crespo A, Estrin DA, Coitiño EL. Structural and Energetic Study of Cisplatin and Derivatives: Comparison of the Performance of Density Funtional Theory Implementations. J Chem Theory Comput 2008; 4:740-50. [DOI: 10.1021/ct7002385] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pablo D. Dans
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Centro Universitario Malvín Norte, Iguá 4225, Montevideo 11400, Uruguay, and Departamento de Química Inorgánica, Analítica y Química Física/IUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Alejandro Crespo
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Centro Universitario Malvín Norte, Iguá 4225, Montevideo 11400, Uruguay, and Departamento de Química Inorgánica, Analítica y Química Física/IUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - Darío A. Estrin
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Centro Universitario Malvín Norte, Iguá 4225, Montevideo 11400, Uruguay, and Departamento de Química Inorgánica, Analítica y Química Física/IUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
| | - E. Laura Coitiño
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República (UdelaR), Centro Universitario Malvín Norte, Iguá 4225, Montevideo 11400, Uruguay, and Departamento de Química Inorgánica, Analítica y Química Física/IUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, Buenos Aires (C1428EHA), Argentina
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20
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Noguera M, Bertran J, Sodupe M. Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes. J Phys Chem B 2008; 112:4817-25. [PMID: 18358032 DOI: 10.1021/jp711982g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.
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Affiliation(s)
- Marc Noguera
- Departament de Química, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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21
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Bradác O, Zimmermann T, Burda JV. Comparison of the electronic properties, and thermodynamic and kinetic parameters of the aquation of selected platinum(II) derivatives with their anticancer IC50 indexes. J Mol Model 2008; 14:705-16. [PMID: 18322710 DOI: 10.1007/s00894-008-0285-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 02/06/2008] [Indexed: 11/28/2022]
Abstract
Three potential anticancer agents {trans-[PtCl(2)(NH(3))(thiazole)], cis-[PtCl(2)(NH(3))(piperidine)], and PtCl(2)(NH(3))(cyclohexylamine) (JM118)} were explored and compared with cisplatin and the inactive [PtCl(dien)](+) complex. Basic electronic properties, bonding and stabilization energies were determined, and thermodynamic and kinetic parameters for the aquation reaction were estimated at the B3LYP/6-311++G(2df,2pd) level of theory. Since the aquation process represents activation of these agents, the obtained rate constants were compared with the experimental IC(50) values for several tumor cells. Despite the fact that the processes in which these drugs are involved and the way in which they affect cells are very complex, some correlations can be deduced.
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Affiliation(s)
- Ondrej Bradác
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
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22
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Kosenkov D, Gorb L, Shishkin OV, Sponer J, Leszczynski J. Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+. J Phys Chem B 2007; 112:150-7. [PMID: 18069814 DOI: 10.1021/jp075888t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ and B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. The Mg2+ ion forms two inner-shell contacts with the nucleotide, similar to small phosphorylated molecules under physiological conditions. The presence of the phosphate group and the hydrated magnesium cation leads to a change in guanine tautomeric equilibrium of 4H2O.Mg[dGMP] in comparison to free guanine. The influence of the phosphate group and the magnesium cation on tautomeric equilibrium is larger in the anti conformation where the P=O-->Mg and Mg<--N7 coordinate bonds are formed. The canonical oxo form of guanine is more stable (by 6-8 kcal/mol) than the O6-hydroxo form in anti conformation. Thus, the interaction with Mg2+ ion is capable of further suppressing the likelihood of a spontaneous transient formation of the rare tautomer. In the syn conformation of 4H2O.Mg[dGMP], the interaction of the guanine nucleobase with the phosphate group and the magnesium cation is not as strong as in the anti conformation, and the relative stability of guanine tautomers is close to those in free guanine.
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Affiliation(s)
- Dmytro Kosenkov
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, USA
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Matsui T, Shigeta Y, Hirao K. Multiple Proton-Transfer Reactions in DNA Base Pairs by Coordination of Pt Complex. J Phys Chem B 2007; 111:1176-81. [PMID: 17266272 DOI: 10.1021/jp065727+] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The possibility of multiple proton-transfer reactions in DNA base pairs because of coordination of cisplatin is theoretically elucidated by density functional theory (DFT) and by quantum mechanics/molecular mechanics (QM/MM) methods with an ONIOM method. From the energetics of two base pairs with the cisplatin, it is theoretically confirmed that the Pt complex is likely to bind in the order cis-(CG)-Pt-(GC), cis-(CG)-Pt-(AT), cis-(TA)-Pt-(AT), where G, C, A, and T are guanine, cytosine, adenine, and thymine, respectively, and the Pt atom bonds to the N7 site of G and A. This result supports the experimental evidence, where the structure cis-A-Pt-A is seldom observed at room temperature. The single proton-transfer reaction occurs in one of the two GC pairs. No simultaneous single proton-transfer reaction can occur in both base pairs. Two different single proton-transferred structures (cis-(CG*)(d)-Pt-(GC)(p) and cis-(CG)(d)-Pt-(G*C)(p), where the asterisk means a proton donor of G) are as stable as the original structures (CG)(d)-Pt-(GC)(p). The same tendency was observed with cis-(CG*)-Pt-(AT). In contrast to cisplatin, multiple single proton-transfer reactions occur in the system consisting of two base pairs with transplatin. The optimized structure agrees with the experimental data for Pt-G coordination except for the hydrogen-bonding length.
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Affiliation(s)
- Toru Matsui
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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24
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Xing D, Chen X, Bu Y. Pairing strength and proton characters of the N7,N9-dimethylated GC and AT base pairs: a density functional theory investigation. NEW J CHEM 2007. [DOI: 10.1039/b702640d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Pavelka M, Burda JV. Pt-bridges in various single-strand and double-helix DNA sequences. DFT and MP2 study of the cisplatin coordination with guanine, adenine, and cytosine. J Mol Model 2006; 13:367-79. [PMID: 17024406 DOI: 10.1007/s00894-006-0151-x] [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] [Received: 12/28/2005] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
In this study, various platinum cross-links in DNA bases were explored. Some of these structures occur in many cis/trans-platinated double-helixes or single-stranded adducts. However, in the models studied, no steric hindrance from sugar-phosphate backbone or other surroundings is considered. Such restrictions can change the bonding picture partially but hopefully the basic energy characteristics will not be changed substantially. The optimization of the structures explored was performed at the DFT level with the B3LYP functional and the 6-31G(d) basis set. Perturbation theory at the MP2/6-31++G(2df,2pd) level was used for the single-point energy and 6-31+G(d) basis set for the electron-property analyses. It was found that the most stable structures are the diguanine complexes followed by guanine-cytosine Pt-cross-links, ca 5 kcal mol(-1) less stable. The adenine-containing complexes are about 15 kcal mol(-1) below the stability of diguanine structures. This stability order was also confirmed by the BE of Pt-N bonds. For a detailed view on dative and electrostatic contributions to Pt-N bonds, Natural Population Analysis, determination of electrostatic potentials, and canonical Molecular Orbitals description of the examined systems were used.
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Affiliation(s)
- Matej Pavelka
- Faculty of Mathematics and Physics, Department of Chemical Physics and Optics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
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26
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Liang W, Li H, Hu X, Han S. Systematic theoretical investigations on all of the tautomers of guanine: From both dynamics and thermodynamics viewpoint. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.06.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Lau JKC, Deubel DV. Loss of amine from platinum(II) complexes: implications for cisplatin inactivation, storage, and resistance. Chemistry 2006; 11:2849-55. [PMID: 15744707 DOI: 10.1002/chem.200401053] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Potential consequences of the binding of the anticancer drug cisplatin to various biomolecules in the cell have been investigated by using a combined density functional theory and continuum dielectric model approach. Since the amine ligands remain coordinated at the metal upon formation of the most frequent DNA adducts, whereas they were found to be displaced from the metal upon formation of drug metabolites, we have analyzed the factors governing amine loss from platinum(II) complexes as a possible pathway of cisplatin inactivation. The calculations systematically show the effect of 1) the trans ligand, 2) the charge of complex, 3) the nucleophile, and 4) the environment on the thermodynamic instability and kinetic lability of the platinum-amine bonds. After initial binding of cisplatin hydrolysis products to thioethers or thiols, loss of the amine trans to this sulfur ligand rather than replacement of the sulfur ligand itself by other nucleophiles like guanine-N7 is predicted to be the predominant reaction. The results of this study contribute to an understanding of the modes of cisplatin inactivation prior to DNA binding, for example, by elevated glutathione levels in cisplatin-resistant cancer cells.
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Affiliation(s)
- Justin Kai-Chi Lau
- ETH Zürich, Department of Chemistry and Applied Biosciences, Computational Science, USI Campus, 6900 Lugano, Switzerland
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28
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Fonseca Guerra C, van der Wijst T, Bickelhaupt FM. Supramolecular Switches Based on the Guanine–Cytosine (GC) Watson–Crick Pair: Effect of Neutral and Ionic Substituents. Chemistry 2006; 12:3032-42. [PMID: 16453355 DOI: 10.1002/chem.200501301] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We have theoretically analyzed Watson-Crick guanine-cytosine (GC) base pairs in which purine-C8 and/or pyrimidine-C6 positions carry a substituent X = NH(-), NH(2), NH(3) (+) (N series), O(-), OH, or OH(2) (+) (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. The purpose is to study the effects on structure and hydrogen-bond strength if X= H is substituted by an anionic, neutral, or cationic substituent. We found that replacing X = H by a neutral substituent has relatively small effects. Introducing a charged substituent, on the other hand, led to substantial and characteristic changes in hydrogen-bond lengths, strengths, and hydrogen-bonding mechanism. In general, introducing an anionic substituent reduces the hydrogen-bond-donating and increases the hydrogen-bond-accepting capabilities of a DNA base, and vice versa for a cationic substituent. Thus, along both the N and O series of substituents, the geometric shape and bond strength of our DNA base pair can be chemically switched between three states, thus yielding a chemically controlled supramolecular switch. Interestingly, the orbital-interaction component in some of these hydrogen bonds was found to contribute to more than 49 % of the attractive interactions and is thus virtually equal in magnitude to the electrostatic component, which provides the other (somewhat less than) 51 % of the attraction.
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Affiliation(s)
- Célia Fonseca Guerra
- Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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29
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Zimmermann T, Zeizinger M, Burda JV. Cisplatin interaction with cysteine and methionine, a theoretical DFT study. J Inorg Biochem 2005; 99:2184-96. [PMID: 16183131 DOI: 10.1016/j.jinorgbio.2005.07.021] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 07/29/2005] [Accepted: 07/30/2005] [Indexed: 10/25/2022]
Abstract
Interactions of hydrated cisplatin complexes with sulphur-containing amino acids cysteine and methionine were explored. The square-planar cis-[Pt(NH3)2(H2O)X]+ complexes (where X=Cl- and OH-) were chosen as mono- and dihydrated reactants. Calculations using density functional theory (DFT) techniques with B3LYP functional were performed. The isolated molecules and the supermolecular approaches were employed for the determination of the reaction energies. Bond dissociation energies (BDE) were estimated in the model of isolated molecules and supermolecules were used for the determination of the association energies between the two interacting parts. Formation of monodentate complexes by replacing the aqua-ligand with the S, N, and O-sites of both amino acids represents an exothermic process. The highest BDE was found in cysteine structures for the Pt-S coordination. The bonding energy is about 114 kcal/mol, which is comparable with cisplatin-guanine adducts. Analogous BDE for methionine complexes is smaller by about 40 kcal/mol. This correlates well with the known fact that cysteine forms irreversible cisplatin adducts while similar adducts in the methionine case are reversible. The formation of chelate structures is an exothermic reaction only for the hydroxo-form of reactants in the supermolecular approach where additional association interactions between the released water and chelate molecules sufficiently stabilize the final product.
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Affiliation(s)
- Tomás Zimmermann
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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30
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Brauer B, Gerber RB, Kabelác M, Hobza P, Bakker JM, Abo Riziq AG, de Vries MS. Vibrational Spectroscopy of the G· · ·C Base Pair: Experiment, Harmonic and Anharmonic Calculations, and the Nature of the Anharmonic Couplings. J Phys Chem A 2005; 109:6974-84. [PMID: 16834057 DOI: 10.1021/jp051767m] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels of electronic structure theory. Anharmonic frequencies were obtained by the CC-VSCF method with improved PM3 potential surfaces; the improved PM3 potential surfaces are obtained from standard PM3 theory by coordinate scaling such that the improved PM3 harmonic frequencies are the same as those computed at the RI-MP2/cc-pVDZ level. Comparison of the data with experimental results indicates that the average absolute percentage deviation for the methods is 2.6% for harmonic RI-MP2/cc-pVDZ (3.0% with the inclusion of a 0.956 scaling factor that compensates for anharmonicity), 2.5% for harmonic RI-MP2/TZVPP (2.9% with a 0.956 anharmonicity factor included), and 2.3% for adapted PM3 CC-VSCF; the empirical scaling factor for the ab initio harmonic calculations improves the stretching frequencies but decreases the accuracy of the other mode frequencies. The agreement with experiment supports the adequacy of the improved PM3 potentials for describing the anharmonic force field of the G...C base pair in the spectroscopically probed region. These results may be useful for the prediction of the pathways of vibrational energy flow upon excitation of this system. The anharmonic calculations indicate that anharmonicity along single mode coordinates can be significant for simple stretching modes. For several other cases, coupling between different vibrational modes provides the main contribution to anharmonicity. Examples of strongly anharmonically coupled modes are the symmetric stretch and group torsion of the hydrogen-bonded NH2 group on guanine, the OH stretch and torsion of the enol group on cytosine, and the NH stretch and NH out-of-plane bend of the non-hydrogen-bonded NH group on guanine.
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Affiliation(s)
- Brina Brauer
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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31
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Burda JV, Zeizinger M, Leszczynski J. Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT andab initio computational study of thermodynamic and kinetic parameters. J Comput Chem 2005; 26:907-14. [PMID: 15841473 DOI: 10.1002/jcc.20228] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The thermodynamic and kinetic aspects of hydration reactions of cis-/transplatin were explored. The polarizable continuum model was used for estimation of solvent effects. Using the B3LYP/6-31+G(d) method, the structures were optimized and vibrational frequencies estimated. Interaction energies and activation barriers were determined at the CCSD(T)/6-31++G(d,p) level within the COSMO approach. An associative mechanism was assumed with a trigonal-bipyramidal structure of the transition state. Within the applied model, all the hydration reactions are slightly endothermic. The Gibbs energies of cisplatin hydration amount to 7.0 and 14.2 kcal/mol for the chloride and ammonium replacement, respectively. Analogous values for the transplatin reactions are 6.8 and 11.9 kcal/mol. The determined rate constants are by several (three to four) orders of magnitude larger for the dechlorination process than for deammination. The cisplatin dechlorination rate constant was established as 1.3 x 10(-4) s(-1) in excellent accord with the experiment.
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Affiliation(s)
- Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic.
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32
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Robertazzi A, Platts JA. Hydrogen Bonding and Covalent Effects in Binding of Cisplatin to Purine Bases: Ab Initio and Atoms in Molecules Studies. Inorg Chem 2004; 44:267-74. [PMID: 15651872 DOI: 10.1021/ic0489544] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio and density functional calculations are employed to investigate the role of hydrogen bonding in the binding of cisplatin to the purine bases guanine and adenine. Through the use of the theory of atoms in molecules (AIM), it is shown that hydrogen bonds are ubiquitous in such systems, with N-H...N and N-H...Cl interactions present in addition to the expected N-H...O. This in turn means that the known stability of cisplatin-guanine complexes cannot be ascribed solely to hydrogen bonding and allows decomposition of total binding energy into contributions from covalent and hydrogen bonds. To do so, a new method for predicting hydrogen bond energies from bond critical point properties is proposed, employing partial least-squares analysis to remove the family dependence of simple models. Still more hydrogen bond motifs are found in bifunctional complexes of the general type purine-[Pt(NH(3))(2)](2+)-purine, including purine...purine contacts, though again the energetics of these are insufficient to explain the observed trends in stability. Finally, the effect of platination on the pairing of guanine with cytosine is studied in a similar manner, revealing large redistributions of hydrogen bonding but surprisingly small overall changes in pairing energy.
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Affiliation(s)
- Arturo Robertazzi
- Department of Chemistry, Cardiff University, P.O. Box 912, Cardiff CF10 3TB, UK
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33
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Gu J, Wang J, Leszczynski J. H−Bonding Patterns in the Platinated Guanine−Cytosine Base Pair and Guanine−Cytosine−Guanine−Cytosine Base Tetrad: an Electron Density Deformation Analysis and AIM Study. J Am Chem Soc 2004; 126:12651-60. [PMID: 15453799 DOI: 10.1021/ja0492337] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The atoms in molecule theory (AIM) and electronic structure analysis are applied together to investigate H-bonding patterns in metalated nucleobase complexes. The influence of Pt on the intra GC base pair H-bonding has been found to reduce intra base pair H-bonding of N4(C)...O6(G) in the platinated GC pair and GCGC tetrad. The relaxation of geometry constrains in metalated nucleobases is found to be decisively important in the formation of novel molecular architectures from nucleobases and metal entities. The incorporation of the platinum in the GCGC tetrad benefits the formation of the unique CH...N (H5(C)...N1(G)) hydrogen bond pattern in the tetrad by offering improved geometric constraints rather than through changing the electronic properties around the H5(C) and N1(G) sites. Platination at the N7 of guanine reduces the deprotonation energy considerably.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, PR China.
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34
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Robertazzi A, Platts JA. Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study. J Comput Chem 2004; 25:1060-7. [PMID: 15067681 DOI: 10.1002/jcc.20038] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Density functional calculations on a range of hydrogen bonded clusters of cisplatin are reported. A systematic search of 1:1 cisplatin:water complexes reveals only three stable minima, which contain a number of common, recurring interactions, such as an N-H...O-H...Cl bridging mode. Expanding these clusters by adding water molecules leads to a model of the first solvation shell of cisplatin, which contains the above motifs along with several strong water-water interactions. The strengths of such interactions are rationalized on the basis of electrostatic potentials, and quantified by use of Atoms in Molecules properties. This analysis also allows us to estimate cisplatin's position on Abraham's hydrogen bond acidity and basicity scales, indicating that cisplatin is a strong donor and acceptor of hydrogen bonds due to the dominance of hard, electrostatic interactions. The effects of this explicit solvation on the barrier to hydrolysis, and hence activation, of cisplatin are explored, indicating a slightly higher barrier than in the gas phase, leading to better agreement with experiment than either gas phase or continuum solvation calculations.
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Affiliation(s)
- Arturo Robertazzi
- Department of Chemistry, Cardiff University, P.O. Box 912, Cardiff CF10 3TB, UK
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35
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Burda JV, Zeizinger M, Leszczynski J. Activation barriers and rate constants for hydration of platinum and palladium square-planar complexes: An ab initio study. J Chem Phys 2004; 120:1253-62. [PMID: 15268251 DOI: 10.1063/1.1633757] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the present work, an ab initio study on hydration (a metal-ligand replacement by water molecule or OH- group) of cis- and transplatin and their palladium analogs was performed within a neutral pseudomolecule approach (e.g., metal-complex+water as reactant complex). Subsequent replacement of the second ligand was considered. Optimizations were performed at the MP2/6-31+G(d) level with single-point energy evaluation using the CCSD(T)/6-31++G(d,p) approach. For the obtained structures of reactants, transition states (TS's), and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (rate constants) characteristics were estimated. It was found that all the hydration processes are mildly endothermic reactions-in the first step they require 8.7 and 10.2 kcal/mol for ammonium and chloride replacement in cisplatin and 13.8 and 17.8 kcal/mol in the transplatin case, respectively. Corresponding energies for cispalladium amount to 5.2 and 9.8 kcal/mol, and 11.0 and 17.7 kcal/mol for transpalladium. Based on vibrational analyses at MP2/6-31+G(d) level, transition state theory rate constants were computed for all the hydration reactions. A qualitative agreement between the predicted and known experimental data was achieved. It was also found that the close similarities in reaction thermodynamics of both Pd(II) and Pt(II) complexes (average difference for all the hydration reactions are approximately 1.8 kcal/mol) do not correspond to the TS characteristics. The TS energies for examined Pd(II) complexes are about 9.7 kcal/mol lower in comparison with the Pt analogs. This leads to 10(6) times faster reaction course in the Pd cases. This is by 1 or 2 orders of magnitude more than the results based on experimental measurements.
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Affiliation(s)
- Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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36
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Šponer JE, Sychrovský V, Hobza P, Šponer J. Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids. Phys Chem Chem Phys 2004. [DOI: 10.1039/b404306p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Baik MH, Friesner RA, Lippard SJ. cis-{Pt(NH3)2(L)}2+/+ (L = Cl, H2O, NH3) Binding to Purines and CO: Does π-Back-Donation Play a Role? Inorg Chem 2003; 42:8615-7. [PMID: 14686835 DOI: 10.1021/ic035022b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of cis-[Pt(NH(3))(2)(L)](2+/+), a molecular fragment of the anticancer drug cisplatin, to bind to purines and CO by pi-back-donation from Pt to the ligand was examined computationally. Optimized geometries and computed vibrational frequencies suggest that cis-[Pt(NH(3))(2)(L)](2+/+) (L = Cl, H(2)O, NH(3)) is a poor pi-donor and that pi-back-donation does not play an important role for Pt(II)-ligand interactions in general.
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Affiliation(s)
- Mu-Hyun Baik
- Department of Chemistry and School of Informatics, Indiana University, Bloomington, Indiana 47405, USA.
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38
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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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39
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Šponer J, Hobza P. Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies. ACTA ACUST UNITED AC 2003. [DOI: 10.1135/cccc20032231] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.
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