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Rezaei-Sameti M, Iraji Borojeni Z. Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations. J Biomol Struct Dyn 2022:1-12. [PMID: 35866624 DOI: 10.1080/07391102.2022.2099976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahdi Rezaei-Sameti
- Department of Applied Chemistry, Faculty of Science, Malayer University, Malayer, Iran
| | - Zohre Iraji Borojeni
- Department of Applied Chemistry, Faculty of Science, Malayer University, Malayer, Iran
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2
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Samanta A, Mitra I, Reddy B. VP, Mukherjee S, Mahata S, Linert W, Misini B, Bhattacharjee A, Dhabal S, Ghosh GK, Moi SC. Kinetics and mechanism of interaction of Pt(II) complex with bio-active ligands and in vitro Pt(II)-sulfur adduct formation in aqueous medium: bio-activity and computational study. J COORD CHEM 2017. [DOI: 10.1080/00958972.2017.1283025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Avradeep Samanta
- Department of Chemistry, National Institute of Technology, Durgapur, India
| | - Ishani Mitra
- Department of Chemistry, National Institute of Technology, Durgapur, India
| | | | - Subhajit Mukherjee
- Department of Chemistry, National Institute of Technology, Durgapur, India
| | - Sujay Mahata
- Department of Chemistry, National Institute of Technology, Durgapur, India
| | - Wolfgang Linert
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Vienna, Austria
| | - Bashkim Misini
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Vienna, Austria
| | | | - Sukhamoy Dhabal
- Department of Bio-Technology, National Institute of Technology, Durgapur, India
| | - Goutam Kr. Ghosh
- Department of Chemistry, National Institute of Technology, Durgapur, India
| | - Sankar Ch. Moi
- Department of Chemistry, National Institute of Technology, Durgapur, India
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Ray S, Karmakar P, Chattopadhyay A, Nandi D, Sarkar Sain R, Ghosh AK. Kinetic and Mechanistic Investigations on SomeN,N-Chelated Pt(II) Oxalate Complexes with Some “S” Containing Biorelevant Ligands at Physiological Condition. INT J CHEM KINET 2016. [DOI: 10.1002/kin.20995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sumon Ray
- Department of Chemistry; The University of Burdwan; Burdwan 713 104 India
| | - Parnajyoti Karmakar
- Department of Chemistry; Durgapur Government College; Durgapur 713 214 India
| | | | - Debabrata Nandi
- Department of Chemistry; The University of Burdwan; Burdwan 713 104 India
| | - Roshni Sarkar Sain
- Department of Chemistry; The University of Burdwan; Burdwan 713 104 India
| | - Alak K Ghosh
- Department of Chemistry; The University of Burdwan; Burdwan 713 104 India
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Corinti D, Coletti C, Re N, Chiavarino B, Crestoni ME, Fornarini S. Cisplatin Binding to Biological Ligands Revealed at the Encounter Complex Level by IR Action Spectroscopy. Chemistry 2016; 22:3794-803. [DOI: 10.1002/chem.201504521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Cecilia Coletti
- Dipartimento di Farmacia; Università G. D'Annunzio; Via dei Vestini 31 66100 Chieti Italy
| | - Nazzareno Re
- Dipartimento di Farmacia; Università G. D'Annunzio; Via dei Vestini 31 66100 Chieti Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco; Università degli Studi di Roma La Sapienza; P. le A. Moro 5 00185 Roma Italy), Fax
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Banerjee S. Understanding the ring-opening, chelation and non-chelation reactions between nedaplatin and thiosulfate: a DFT study based on NBO, ETS-NOCV and QTAIM. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1772-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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6
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Khusi BB, Mambanda A, Jaganyi D. The role of substituents in a bidentate N,N-chelating ligand on the substitution of aqua ligands from mononuclear Pt(II) complexes. TRANSIT METAL CHEM 2015. [DOI: 10.1007/s11243-015-0011-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Esteves LF, Dos Santos HF, Costa LAS. The conformation effect of the diamine bridge on the stability of dinuclear platinum(II) complexes and their hydrolysis. J Mol Graph Model 2015; 61:290-6. [PMID: 26318233 DOI: 10.1016/j.jmgm.2015.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 11/26/2022]
Abstract
In this paper, the hydrolysis process of a bisplatinum complex containing the flexible chain 1,6-hexanediamine between the two metal centers was investigated through the use of density functional theory (DFT) with the analysis of the role of the spacing group arrangement on the values of free energy activation barrier. All structures were fully optimized in aqueous solution using implicit model for solvent at DFT level. The energy profiles for the hydrolysis reaction were determined by using the supermolecule approach. Five transition states were proposed differing by the conformation of the bridge group, and the activation free energy calculated as a weighted average within the selected forms. The Gibbs population for reactant was used as a statistical weight leading to the predicted value of 23.1kcalmol(-1), in good accordance with experiment, 23.8kcalmol(-1). Our results suggests that for 1,6-hexanediamine bridge ligand, the extend forms with average torsional angle over the carbon chain larger than 130° have the greatest contribution to the hydrolysis kinetics. The results presented here point out that the hydrolysis mechanism might follow different paths for each conformation and each of these contributes to the observed energy barrier.
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Affiliation(s)
- Lucas F Esteves
- NEQC (Núcleo de Estudos em Química Computacional), Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário Martelos, 36036-900 Juiz de Fora, MG, Brazil
| | - Hélio F Dos Santos
- NEQC (Núcleo de Estudos em Química Computacional), Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário Martelos, 36036-900 Juiz de Fora, MG, Brazil
| | - Luiz Antônio S Costa
- NEQC (Núcleo de Estudos em Química Computacional), Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário Martelos, 36036-900 Juiz de Fora, MG, Brazil.
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Shoukry MM, Ezzat SM. Speciation studies of mono- and binuclear Pd(II) complexes involving mixed nitrogen–sulfur donor ligand and 4,4′-bipiperidine as a linker. J COORD CHEM 2015. [DOI: 10.1080/00958972.2015.1043909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Mohamed M. Shoukry
- Faculty of Science, Department of Chemistry, University of Cairo, Cairo, Egypt
| | - Sameya M.T. Ezzat
- Faculty of Science, Department of Chemistry, University of Cairo, Cairo, Egypt
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Palladium(II) Complexes Containing Mixed Nitrogen-Sulphur Donor Ligands: Interaction of [Pd(Methionine Methyl Ester)(H2O)2](2+) with Biorelevant Ligands. Bioinorg Chem Appl 2014; 2014:382646. [PMID: 25214826 PMCID: PMC4158289 DOI: 10.1155/2014/382646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/21/2014] [Indexed: 11/17/2022] Open
Abstract
Pd(MME)Cl2 complex (MME = methionine methyl ester) was synthesised and characterized by physicochemical measurements. The reaction of [Pd(MME)(H2O)2]2+ with amino acids, peptides, or dicarboxylic acids was investigated at 25°C and 0.1 M ionic strength. Amino acids and dicarboxylic acids form 1 : 1 complexes. Peptides form both 1 : 1 complexes and the corresponding deprotonated amide species. The stability of the complexes formed was determined and the binding centres of the ligands were assigned. Effect of solvent on the stability constant of Pd(MME)-CBDCA complex, taken as a representative example, shows that the complex is more favoured in a medium of low dielectric constant. The concentration distribution diagrams of the complexes were evaluated.
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Hochreuther S, Nandibewoor ST, Puchta R, van Eldik R. Thermodynamic and kinetic behaviour of [Pt(2-methylthiomethylpyridine)(OH2)2]2+. Dalton Trans 2012; 41:512-22. [DOI: 10.1039/c1dt11453k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Anconi CP, da Silva Delgado L, Alves dos Reis JB, De Almeida WB, Costa LAS, Dos Santos HF. Inclusion complexes of α-cyclodextrin and the cisplatin analogues oxaliplatin, carboplatin and nedaplatin: A theoretical approach. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study. J Mol Model 2011; 17:2385-93. [DOI: 10.1007/s00894-011-1031-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/06/2011] [Indexed: 10/18/2022]
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13
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Aguilar CM, Rocha WR. Ligand Exchange Reaction Involving Ru(III) Compounds in Aqueous Solution: A Hybrid Quantum Mechanical/Effective Fragment Potential Study. J Phys Chem B 2011; 115:2030-7. [DOI: 10.1021/jp110198h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Charles M. Aguilar
- Departamento de Química, ICEX, Universidade Federal de Minas Gerais 31270-901, Pampulha, Belo Horizonte, MG, Brazil
| | - Willian R. Rocha
- Departamento de Química, ICEX, Universidade Federal de Minas Gerais 31270-901, Pampulha, Belo Horizonte, MG, Brazil
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Yokogawa D, Ono K, Sato H, Sakaki S. Theoretical study on aquation reaction of cis-platin complex: RISM–SCF–SEDD, a hybrid approach of accurate quantum chemical method and statistical mechanics. Dalton Trans 2011; 40:11125-30. [DOI: 10.1039/c1dt10703h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Zhang D, Ren X, Zhou L. Theoretical analysis of trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to biological targets — Factors influence binding kinetics and adduct stability. CAN J CHEM 2010. [DOI: 10.1139/v10-139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Full reaction energy profiles for trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to sulfur- and nitrogen-containing biorelevant ligands were constructed by the density functional theory (DFT) method. Calculated results demonstrate that trans-platinum complexes can interact with biological targets, affording cis and trans products via very similar transition states. For different substituents, sulfur-containing ligands constitute kinetically preferred targets for platination, whereas the platination of nitrogen-containing ligands is more favorable thermodynamically. This is consistent with previous experimental studies. Calculated results also suggest that the trans effect, the influence of the ligand, the size of the ligand, and hydrogen bonding play important roles in binding kinetics and stabilizing adducts.
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Affiliation(s)
- Dongdong Zhang
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Xiuli Ren
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Lixin Zhou
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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16
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Comparative study of the hydrolysis of a third- and a first-generation platinum anticancer complexes. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0825-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Hydrolysis and binding mechanism of AMD473 (cis-[PtCl2(NH3)(2-picoline)]) with guanine: A quantum mechanical study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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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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Yoshikawa A, Bach SBH, Merrill GN. An experimental and theoretical investigation into the hydrolysis of dichloro(ethylenediamine)platinum(II) via electrospray mass spectrometry and density functional theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:1015-1029. [PMID: 19285881 DOI: 10.1016/j.jasms.2008.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 11/28/2008] [Accepted: 11/30/2008] [Indexed: 05/27/2023]
Abstract
Dichloro(ethylenediamine)platinum(II), Pt(en)Cl(2), was dissolved in H(2)O and D(2)O, and the resulting aqueous solutions were electrosprayed into a quadrupole ion-trap mass spectrometer. A series of major and minor ionic hydrolysis products were detected. These ions were then subjected to collision-induced dissociation. As an aid in interpreting the experimental results, density functional theory calculations were carried out. These computations permitted the structures and energetics associated with the hydrolysis products to be determined. An understanding of the hydrolysis of PtenCl(2) and related coordination complexes is essential in the rational design of metal-based drugs.
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Affiliation(s)
- Akihiko Yoshikawa
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, San Antonia, Texas 78249, USA
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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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Characterization and DNA interaction of the Pt(II)(pq)(bdt) complex: A theoretical and experimental research. Inorganica Chim Acta 2008. [DOI: 10.1016/j.ica.2007.10.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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22
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Lopes JF, Rocha WR, Dos Santos HF, De Almeida WB. Theoretical study of the potential energy surface for the interaction of cisplatin and their aquated species with water. J Chem Phys 2008; 128:165103. [DOI: 10.1063/1.2909979] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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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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Mitsopoulou CA, Dagas CE, Makedonas C. Synthesis, characterization, DFT studies and DNA binding of mixed platinum (II) complexes containing quinoxaline and 1,2-dithiolate ligands. J Inorg Biochem 2007; 102:77-86. [PMID: 17709143 DOI: 10.1016/j.jinorgbio.2007.07.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Revised: 07/02/2007] [Accepted: 07/05/2007] [Indexed: 11/20/2022]
Abstract
The complexes Pt(pq)Cl2(1) and Pt(pq)(bdt) (2) (where pq = 2-(2'pyridyl)quinoxaline and bdt=benzene-1,2-dithiolate) have been synthesized and fully characterized by UV-visible (UV-Vis), Fourier Transformer Infrared Spectra (FTIR), 1 and 2D NMR and cyclic voltammetry (CV). Interactions of the tested systems (the aforementioned complexes 1 and 2) and the free ligands pq and bdt with double stranded calf thymus DNA (CT-DNA) were studied by UV-spectrophotometric (melting curves) and circular dichroism (CD) measurements. The results suggest that both complexes 1 and 2, are able to form adducts with DNA and to distort the double helix by changing the base stacking. Complex 2 forms stronger adducts to CT-DNA than complex 1 and this is probably due to the substitution of the chlorine atoms of 1 by the 1,2-dithiolate ligand (bdt) in 2. The latter induces an extensive distortion in the planarity of 2 as density functional theory (DFT) calculations reveal. Besides, the light absorbing complex 2 possess intense mixed metal ligand to ligand charge transfer (MM'LLCT) transition in the visible region of the spectrum and could act as photoluminescent metal-based probe for the study of DNA binding. Thus, the photocleavage of DNA by 2 has been studied by UV-Vis and CD spectra and monitored by agarose gel electrophoresis. Under our experimental conditions, it is unclear that complex 2 can photocleave DNA. Furthermore, the ability of 2 to inhibit proliferation of human tumor cell lines was tested and the results indicate some cytoxytic effect on the SF-286 cells.
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Affiliation(s)
- Christiana A Mitsopoulou
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece.
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25
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Ozimiński WP, Garnuszek P, Bednarek E, Dobrowolski JC. The platinum complexes with histamine: Pt(II)(Hist)Cl2, Pt(II)(Iodo-Hist)Cl2 and Pt(IV)(Hist)2Cl2. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Wysokiński R, Hernik K, Szostak R, Michalska D. Electronic structure and vibrational spectra of cis-diammine(orotato)platinum(II), a potential cisplatin analogue: DFT and experimental study. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.01.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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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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Lopes JF, de A Menezes VS, Duarte HA, Rocha WR, De Almeida WB, Dos Santos HF. Monte Carlo Simulation of Cisplatin Molecule in Aqueous Solution. J Phys Chem B 2006; 110:12047-54. [PMID: 16800515 DOI: 10.1021/jp057448c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Lennard-Jones (12-6) parameters were obtained for all atoms of cisplatin molecule using the ab initio quantum mechanical potential energy surface for the water-cisplatin interaction as reference data. The parameters found were (epsilon/kcal.mol(-1) and sigma/angstroms) 1.0550, 3.6590 (Pt); 0.0381, 4.6272 (Cl); 0.0455, 3.3783 (N); and 0.0185, 0.0936 (H) and provided very good results for the description of the aqueous solution of cisplatin through Monte Carlo simulation. From statistical analysis of solute-solvent interactions, we observed that the NH3 groups are involved in 53% of the calculated hydrogen bonds with a significant contribution from chlorides (41%) and only 6% involving the Pt center. This is in agreement with the expected behavior for such molecules. Two hydration shells with 22 and 81 water molecules, respectively, centered around 4.6 and 7.3 angstroms were found from the center of mass pair correlation function analysis. The cisplatin atomic Lennard-Jones parameters are reported for the first time, and they might be useful for studying the structure, properties, and processes of cisplatin-like molecules in aqueous solution, including explicitly the solvent effect.
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Affiliation(s)
- Juliana Fedoce Lopes
- NEQC: Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Martelos, CEP 36036-900, Juiz de Fora, MG, Brazil
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Spiegel K, Magistrato A. Modeling anticancer drug–DNA interactions via mixed QM/MM molecular dynamics simulations. Org Biomol Chem 2006; 4:2507-17. [PMID: 16791311 DOI: 10.1039/b604263p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of anticancer drugs started over four decades ago, with the serendipitous discovery of the antitumor activity of cisplatin and its successful use in the treatment of various cancer types. Despite the efforts made in unraveling the mechanism of the action of cisplatin, as well as in the rational design of new anticancer compounds, in many cases detailed structural and mechanistic information is still lacking. Many of these drugs exert their anticancer activity by covalently binding to DNA inducing a distortion or simply impeding replication, thus triggering a cellular response, which eventually leads to cell death. A detailed understanding of the structural and electronic properties of drug-DNA complexes and their mechanism of binding is the key step in elucidating the principles of their anticancer activity. At the theoretical level, the description of covalent drug-DNA complexes requires the use of state-of-the-art computer simulation techniques such as hybrid quantum/classical molecular dynamics simulations. In this review we provide a general overview on: drugs which covalently bind to DNA duplexes, the basic concepts of quantum mechanics/molecular mechanics (QM/MM), molecular dynamics methods and a list of selected applications of these simulations to the study of drug-DNA adducts. Finally, the potential and the limitations of this approach to the study of such systems are critically evaluated.
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Affiliation(s)
- Katrin Spiegel
- University of Pennsylvania, Department of Chemistry, Philadelphia, PA, USA
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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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Yang G, Han X, Zhang W, Liu X, Yang P, Zhou Y, Bao X. Study on Conformation Interconversion of 3-Alkyl-4-acetyl-3,4-dihydro-2H-1,4-benzoxazines from Dynamic NMR Experiments and ab Initio Density Functional Calculations. J Phys Chem B 2005; 109:18690-8. [PMID: 16853404 DOI: 10.1021/jp050874d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Variable-temperature NMR experiments and ab initio density functional calculations were carried out to investigate the conformation interconversion of novel chiral 3-alkyl-3,4-dihydro-2H-benzo[1,4]oxazine derivatives. With CDCl3 as the solvent, the coalescence temperatures of H2, H3, H11, and H19 of product 1 are about 289, 304, 292, and 316 K, with the corresponding activation free energies at 58.0 +/- 6.7, 60.9 +/- 7.1, 58.3 +/- 6.8, and 59.6 +/- 6.9 kJ.mol(-1), respectively. When dimethyl sulfoxide (DMSO-d6) was used as the solvent, 1H and 13C NMR signals were completely assigned at 375 K. The effects of solvent and temperature were investigated through a polarizable continuum model. At each theoretical level (MP2 or B3LYP), the changing tendencies of the calculated activation free energies and interconversion rates agree well with those of the NMR results. In addition, the interconversion rate at each specified temperature was calculated to be about 1.5 times faster in DMSO-d6 than in CDCl3. Accordingly, we failed to observe the coalescence phenomena of H3 and H19 in DMSO-d6 by NMR measurements from 296 to 375 K. The substitution effect at the R1-R5 positions was considered using density functional calculations, with the activation barriers decreasing as follows: product 6 > 3 > 1 > 7 > 2. This sequence is consistent with that of the reaction heats, except for product 7, implying that the interconversion processes may be thermodynamically controlled. Surprisingly, the substituted groups near the acetyl group in product 2 and 7 do not elevate the activation barrier but, instead, lower it somewhat, with the possible reasons for this provided in the paper.
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Affiliation(s)
- Gang Yang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People's Republic of China
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Rotzinger FP. Treatment of Substitution and Rearrangement Mechanisms of Transition Metal Complexes with Quantum Chemical Methods. Chem Rev 2005; 105:2003-37. [PMID: 15941208 DOI: 10.1021/cr030715v] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- François P Rotzinger
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland.
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Costa LAS, Rocha WR, De Almeida WB, Dos Santos HF. Linear free energy relationship for 4-substituted (o-phenylenediamine)platinum(II) dichloride derivatives using quantum mechanical descriptors. J Inorg Biochem 2005; 99:575-83. [PMID: 15621292 DOI: 10.1016/j.jinorgbio.2004.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 11/09/2004] [Accepted: 11/12/2004] [Indexed: 11/27/2022]
Abstract
In the present work quantum mechanical methods were used to calculate the rate constants for the first step of the aquation of a set of 4-substituted (o-phenylenediamine)platinum(II) dichloride derivatives containing electron-donating and withdrawing substituents at the 4-position of the aromatic ring. A linear free energy relationship was obtained for log(k(X)/k(H)), k being the rate constant for the first step of hydrolysis, and the electronic Hammett constants sigma(m) and sigma(p). The results showed that electron-donating groups promote the hydrolysis reaction. The quantitative models described here may be useful for the rational design of new, less mutagenic drugs based on platinum complexes.
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Affiliation(s)
- Luiz Antônio S Costa
- Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário Martelos, 36036-330 Juiz de Fora, MG, Brazil
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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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Junqueira GM, Rocha WR, De Almeida WB, Dos Santos HF. Theoretical study of oxocarbons: structure and vibrational spectrum of the D6h and C2 forms of the rhodizonate ion. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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