1
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Almeida ER, Dos Santos HF. Nanoconfinement effect on the hydrolysis of cisplatin. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2022.140247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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2
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Paschoal DFS, Dos Santos HF. Intramolecular force field for carboxylate Pt(II)-complexes. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02901-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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How can the cisplatin analogs with different amine act on DNA during cancer treatment theoretically? J Mol Model 2021; 28:2. [PMID: 34874466 DOI: 10.1007/s00894-021-04984-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/15/2021] [Indexed: 01/04/2023]
Abstract
Cisplatin is a widely used anti-cancer drug which inhibits the replication and polymerization of DNA molecule while showing some side effects and drug resistance. For this reason, to enhance its therapeutic index, researchers have synthesized several thousand analogs and tested their properties. In this project, several cisplatin analogs were designed to theoretically study the biological activity and lipophilicity effects on amine changes. The amines of the cisplatin molecule were substituted with aliphatic amines in different analogs. Computational methods such as molecular dynamics simulation, molecular docking, and molecular mechanics Poisson-Boltzmann surface area analysis were performed to investigate the binding of six cisplatin derivatives with DNA. The binding affinity and potential interactions of these drugs with double-strand DNA were analyzed. The stability effect of these drugs was investigated via root-mean-square deviation and root-mean-square fluctuation analysis, which showed that some analogs can break base-pair interaction at the end of DNA and reduced the stability of DNA. Also, the results revealed that the hydrogen bond is one of the most important factors in the binding of cisplatin's adduct to DNA. Molecular mechanics Poisson-Boltzmann surface area analysis indicated that electrostatic and van der Waals interactions are the most important deriving forces to the binding of cisplatin's drug to DNA. Finally, data revealed that cisplatin and the cis-dichloro-dimethylamine-platin tendency for binding to DNA are greater than that of other analogs.
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4
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de Almeida CA, Pinto LPNM, Dos Santos HF, Paschoal DFS. Vibrational frequencies and intramolecular force constants for cisplatin: assessing the role of the platinum basis set and relativistic effects. J Mol Model 2021; 27:322. [PMID: 34636999 DOI: 10.1007/s00894-021-04937-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022]
Abstract
The role of platinum basis set (PTBS) and relativistic effects for predicting the vibrational frequencies and intramolecular force constants for cisplatin are discussed. Nonrelativistic and relativistic computational protocols were built at B3LYP/PTBS/jorge-DZP/C-PCM and B3LYP-DKH2/PTBS/jorge-DZP-DKH/C-PCM levels, respectively, where 19 distinct PTBS were tested. As expected, the structural parameters were not very sensitive to the PTBS, however, the inclusion of relativistic effects improves the description of the cisplatin structure. When it comes to the vibrational frequencies, the results show that the PTBS, and mainly the relativistic effects, are both important. Moreover, the PBE0 functional led to better results than B3LYP in the protocols PBE0/LANL2TZ(f)/jorge-DZP/C-PCM (P20) and PBE0-DKH2/Sapporo-DKH3-DZP-2012/jorge-DZP-DKH/C-PCM (P22), which provided a mean absolute deviation (MAD) of only 10.8 cm-1 and 9.5 cm-1, respectively, for vibrational frequencies, which are excellent choices to study Pt complexes. Finally, a discussion of the intramolecular force constants for cisplatin is carried out, with the calculated bond and angles force constants with P20 and P22 protocols being recommended for the parameterization of the force field of cisplatin.
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Affiliation(s)
- Caroline A de Almeida
- NQTCM: Núcleo de Química Teórica E Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal Do Rio de Janeiro, 27.973-545, Macaé, RJ, Brazil
| | - Larissa P N M Pinto
- NQTCM: Núcleo de Química Teórica E Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal Do Rio de Janeiro, 27.973-545, Macaé, RJ, Brazil
| | - Hélio F Dos Santos
- NEQC: Núcleo de Estudos Em Química Computacional, Departamento de Química - ICE, Universidade Federal de Juiz de Fora, Campus Universitário, 36.036-900, Juiz de Fora, MG, Brazil
| | - Diego F S Paschoal
- NQTCM: Núcleo de Química Teórica E Computacional de Macaé, Polo Ajuda, Instituto Multidisciplinar de Química, Centro Multidisciplinar UFRJ-Macaé, Universidade Federal Do Rio de Janeiro, 27.973-545, Macaé, RJ, Brazil.
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5
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Maroń AM, Choroba K, Małecki JG, Kula S, Malicka E. Platinum(II) coordination compound with 4′-[4-(dimethylamino)phenyl]-2,2′:6′,2″-terpyridine – The new insight into the luminescence behavior and substituent effect. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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6
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Rivel T, Ramseyer C, Yesylevskyy S. The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin. Sci Rep 2019; 9:5627. [PMID: 30948733 PMCID: PMC6449338 DOI: 10.1038/s41598-019-41903-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
The composition of the plasma membrane of malignant cells is thought to influence the cellular uptake of cisplatin and to take part in developing resistance to this widespread anti-cancer drug. In this work we study the permeation of cisplatin through the model membranes of normal and cancer cells using molecular dynamics simulations. A special attention is paid to lipid asymmetry and cholesterol content of the membranes. The loss of lipid asymmetry, which is common for cancer cells, leads to a decrease in their permeability to cisplatin by one order of magnitude in comparison to the membranes of normal cells. The change in the cholesterol molar ratio from 0% to 33% also decreases the permeability of the membrane by approximately one order of magnitude. The permeability of pure DOPC membrane is 5-6 orders of magnitude higher than one of the membranes with realistic lipid composition, which makes it as an inadequate model for the studies of drug permeability.
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Affiliation(s)
- Timothée Rivel
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France.
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030, Besançon, Cedex, France.,Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028, Kyiv, Ukraine
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7
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Minervini T, Cardey B, Foley S, Ramseyer C, Enescu M. Fate of cisplatin and its main hydrolysed forms in the presence of thiolates: a comprehensive computational and experimental study. Metallomics 2019; 11:833-844. [DOI: 10.1039/c8mt00371h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiolations and bidentations drive the chemical fate of cisplatin compounds in intracellular medium.
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Affiliation(s)
- Thibault Minervini
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Bruno Cardey
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Sarah Foley
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Christophe Ramseyer
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
| | - Mironel Enescu
- Laboratoire Chrono-environnement (UMR CNRS 6249)
- Université de Franche-Comté
- 25030 Besançon
- France
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8
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Nejad MA, Urbassek HM. Diffusion of cisplatin molecules in silica nanopores: Molecular dynamics study of a targeted drug delivery system. J Mol Graph Model 2019; 86:228-234. [PMID: 30390543 DOI: 10.1016/j.jmgm.2018.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 11/24/2022]
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9
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Tsipis AC, Karapetsas IN. Prediction of 195 Pt NMR of photoactivable diazido- and azine-Pt(IV) anticancer agents by DFT computational protocols. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:145-153. [PMID: 27628024 DOI: 10.1002/mrc.4523] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/03/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
195 Pt NMR chemical shifts for a series of large-sized photoactivable anticancer diazido-Pt(IV), homopiperizine-Pt(IV) and multifunctional azine-Pt(IV) complexes hardly to be probed experimentally and by sophisticated four-component and two-component relativistic calculations are predicted with high accuracy by density functional theory computational protocols. The calculated 195 Pt NMR chemical shifts constitute a crucial descriptor for making highly predictive one-parameter quantitative structure activity relationships models that help in designing photoactivable Pt(IV)-based antitumor agents with high cytotoxicity and selectivity. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Athanassios C Tsipis
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - Ioannis N Karapetsas
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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10
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Novato WT, Stroppa PHF, Da Silva AD, Botezine NP, Machado FC, Costa LAS, Dos Santos HF. Reaction between the Pt(II)-complexes and the amino acids of the β-amyloid peptide. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2016.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Cvitkovic JP, Kaminski GA. Developing multisite empirical force field models for Pt(II) and cisplatin. J Comput Chem 2016; 38:161-168. [PMID: 27859392 DOI: 10.1002/jcc.24665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 12/15/2022]
Abstract
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- John P Cvitkovic
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
| | - George A Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, Massachusetts, 01609
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12
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Wheeler OW, Salem M, Gao A, Bakker JM, Armentrout PB. Activation of C-H Bonds in Pt(+) + x CH4 Reactions, where x = 1-4: Identification of the Platinum Dimethyl Cation. J Phys Chem A 2016; 120:6216-27. [PMID: 27438025 DOI: 10.1021/acs.jpca.6b05361] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activation of C-H bonds in the sequential reactions of Pt(+) + x(CH4/CD4), where x = 1-4, have been investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and theoretical calculations. Pt(+) cations are formed by laser ablation and exposed to controlled amounts of CH4/CD4 leading to [Pt,xC,(4x-2)H/D](+) dehydrogenation products. Irradiation of these products in the 400-2100 cm(-1) range leads to CH4/CD4 loss from the x = 3 and 4 products, whereas PtCH2(+)/PtCD2(+) products do not decompose at all, and x = 2 products dissociate only when formed from a higher order product. The structures of these complexes were explored theoretically at several levels of theory with three different basis sets. Comparison of the experimental and theoretical results indicate that the species formed have a Pt(CH3)2(+)(CH4)x-2/Pt(CD3)2(+)(CD4)x-2 binding motif for x = 2-4. Thus, reaction of Pt(+) with methane occurs by C-H bond activation to form PtCH2(+), which reacts with an additional methane molecule by C-H bond activation to form the platinum dimethyl cation. This proposed reaction mechanism is consistent with theoretical explorations of the potential energy surface for reactions of Pt(+) with one and two methane molecules.
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Affiliation(s)
- Oscar W Wheeler
- Department of Chemistry, University of Utah , 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Michelle Salem
- Department of Chemistry, University of Utah , 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Amanda Gao
- Department of Chemistry, University of Utah , 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Joost M Bakker
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University , Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - P B Armentrout
- Department of Chemistry, University of Utah , 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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13
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Tsipis AC, Karapetsas IN. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects? MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:656-664. [PMID: 26990565 DOI: 10.1002/mrc.4426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/22/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
(195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6 - n ](2-) complexes. The simple computational protocol is easily implemented even by synthetic chemists in platinum coordination chemistry that dispose limited software availability, or locally existing routines and knowhow. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Athanassios C Tsipis
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - Ioannis N Karapetsas
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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14
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Markov AA, Yakushev IA, Churakov AV, Stolyarov IP, Cherkashina NV, Kornev AB, Vargaftik MN, Gekhman AE, Moiseev II. Unusual platinum complexes in the gas phase. DOKLADY PHYSICAL CHEMISTRY 2016. [DOI: 10.1134/s0012501616050031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Maroń A, Szlapa A, Czerwińska K, Małecki JG, Krompiec S, Machura B. Solid-state and solution photoluminescence of platinum(ii) complexes with 4′-substituted terpyridine ligands – structural, spectroscopic and electrochemical studies. CrystEngComm 2016. [DOI: 10.1039/c6ce00890a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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He CC, Kimutai B, Bao X, Hamlow L, Zhu Y, Strobehn SF, Gao J, Berden G, Oomens J, Chow CS, Rodgers MT. Evaluation of Hybrid Theoretical Approaches for Structural Determination of a Glycine-Linked Cisplatin Derivative via Infrared Multiple Photon Dissociation (IRMPD) Action Spectroscopy. J Phys Chem A 2015; 119:10980-7. [DOI: 10.1021/acs.jpca.5b08181] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- C. C. He
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - B. Kimutai
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - X. Bao
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - L. Hamlow
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Y. Zhu
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - S. F. Strobehn
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - J. Gao
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - G. Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - J. Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
- van’t
Hoff Institute for Molecular Sciences, University of Amsterdam, 1090 GD Amsterdam, The Netherlands
| | - C. S. Chow
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M. T. Rodgers
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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17
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Yesylevskyy S, Cardey B, Kraszewski S, Foley S, Enescu M, da Silva AM, Dos Santos HF, Ramseyer C. Empirical force field for cisplatin based on quantum dynamics data: case study of new parameterization scheme for coordination compounds. J Mol Model 2015; 21:268. [PMID: 26386959 DOI: 10.1007/s00894-015-2812-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/07/2015] [Indexed: 11/26/2022]
Abstract
Parameterization of molecular complexes containing a metallic compound, such as cisplatin, is challenging due to the unconventional coordination nature of the bonds which involve platinum atoms. In this work, we develop a new methodology of parameterization for such compounds based on quantum dynamics (QD) calculations. We show that the coordination bonds and angles are more flexible than in normal covalent compounds. The influence of explicit solvent is also shown to be crucial to determine the flexibility of cisplatin in quantum dynamics simulations. Two empirical topologies of cisplatin were produced by fitting its atomic fluctuations against QD in vacuum and QD with explicit first solvation shell of water molecules respectively. A third topology built in a standard way from the static optimized structure was used for comparison. The later one leads to an excessively rigid molecule and exhibits much smaller fluctuations of the bonds and angles than QD reveals. It is shown that accounting for the high flexibility of cisplatin molecule is needed for adequate description of its first hydration shell. MD simulations with flexible QD-based topology also reveal a significant decrease of the barrier of passive diffusion of cisplatin accross the model lipid bilayer. These results confirm that flexibility of organometallic compounds is an important feature to be considered in classical molecular dynamics topologies. Proposed methodology based on QD simulations provides a systematic way of building such topologies.
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Affiliation(s)
- S Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, Kiev-28, 03680, Ukraine
| | - Bruno Cardey
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - S Kraszewski
- Department of Biomedical Engineering (W11/K7), Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Sarah Foley
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - Mironel Enescu
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France
| | - Antônio M da Silva
- Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG, 36036-900, Brazil
| | - Hélio F Dos Santos
- Núcleo de Estudos em Química Computacional, Departamento de Química, ICE, Universidade Federal de Juiz de Fora (UFJF), Campus Universitário, Martelos, Juiz de Fora, MG, 36036-900, Brazil
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Franche-Comté, 16 route de Gray, 25030, Besançon Cedex, France.
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18
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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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19
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Martins L, Jorge F, Machado S. All-electron segmented contraction basis sets of triple zeta valence quality for the fifth-row elements. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1040095] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Fiuza SM, Amado AM, Parker SF, Marques MPM, Batista de Carvalho LAE. Conformational insights and vibrational study of a promising anticancer agent: the role of the ligand in Pd(ii)–amine complexes. NEW J CHEM 2015. [DOI: 10.1039/c5nj01088h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study reports the first complete vibrational analysis of a dinuclear polyamine-based compound displaying antitumour properties.
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Affiliation(s)
- Sónia M. Fiuza
- Unidade de I&D “Química-Física Molecular”
- Departamento de Química
- Universidade de Coimbra
- P-3004 535 Coimbra
- Portugal
| | - Ana M. Amado
- Unidade de I&D “Química-Física Molecular”
- Departamento de Química
- Universidade de Coimbra
- P-3004 535 Coimbra
- Portugal
| | | | - Maria Paula M. Marques
- Unidade de I&D “Química-Física Molecular”
- Departamento de Química
- Universidade de Coimbra
- P-3004 535 Coimbra
- Portugal
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21
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Zhang C, Naziga EB, Guidoni L. Asymmetric environmental effects on the structure and vibrations of cis-[Pt(NH3)2Cl2] in condensed phases. J Phys Chem B 2014; 118:11487-95. [PMID: 25144652 DOI: 10.1021/jp500865v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the structural and vibrational properties of anticancer drug cisplatin (cis-[Pt(NH3)2Cl2]) in gas phase, in solid phase, and in aqueous solution using density functional theory (DFT) calculations, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics, and effective normal modes analysis. In contrast with the gas-phase case, asymmetric hydrogen bonding environments are found in both solid phase and aqueous solution. It is shown that the discrepancy of the molecular geometry between previous gas phase calculations and the X-ray crystal structure can be resolved by considering intermolecular hydrogen bonds in the calculations of solid phase. In addition, our simulations in solid phase and aqueous solution reveal that asymmetric environmental effects lead to several spectral features observed in experiments, such as the blue-shift in the N-H stretching region and the frequency splitting of NH3 symmetric deformation modes. Furthermore, a similar decoupling and localization of several vibrational modes of cisplatin is found in solid phase and aqueous solution, in comparison to those of O-H stretching modes of water molecules in liquid water [ J. Phys. Chem. Lett. 2013 , 4 ( 19 ), 3245 - 3250 ].
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Affiliation(s)
- Chao Zhang
- Physics Department, Sapienza-Universita di Roma , P. le A. Moro 5, 00185, Rome, Italy
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22
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Malik M, Wysokiński R, Zierkiewicz W, Helios K, Michalska D. Raman and Infrared Spectroscopy, DFT Calculations, and Vibrational Assignment of the Anticancer Agent Picoplatin: Performance of Long-Range Corrected/Hybrid Functionals for a Platinum(II) Complex. J Phys Chem A 2014; 118:6922-34. [DOI: 10.1021/jp5056254] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Magdalena Malik
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
| | - Rafał Wysokiński
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
| | - Katarzyna Helios
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
| | - Danuta Michalska
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
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23
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Couzijn EPA, Kobylianskii IJ, Moret ME, Chen P. Experimental Gas-Phase Thermochemistry for Alkane Reductive Elimination from Pt(IV). Organometallics 2014. [DOI: 10.1021/om500478y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erik P. A. Couzijn
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Ilia J. Kobylianskii
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marc-Etienne Moret
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Peter Chen
- Laboratorium
für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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24
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Hu P, Luo Q, Li QS, Xie Y, King RB, Schaefer HF. Construction of the Tetrahedral Trifluorophosphine Platinum Cluster Pt4(PF3)8 from Smaller Building Blocks. Inorg Chem 2014; 53:5300-10. [DOI: 10.1021/ic5005243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peigang Hu
- MOE Key Laboratory of Theoretical Environmental
Chemistry, Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P. R. China
| | - Qiong Luo
- MOE Key Laboratory of Theoretical Environmental
Chemistry, Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P. R. China
| | - Qian-shu Li
- MOE Key Laboratory of Theoretical Environmental
Chemistry, Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P. R. China
| | - Yaoming Xie
- Department of Chemistry and Center for
Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - R. Bruce King
- MOE Key Laboratory of Theoretical Environmental
Chemistry, Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, P. R. China
- Department of Chemistry and Center for
Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F. Schaefer
- Department of Chemistry and Center for
Computational Chemistry, University of Georgia, Athens, Georgia 30602, United States
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25
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Tavares T, Paschoal D, Motta E, Carpanez A, Lopes M, Fontes E, Dos Santos H, Silva H, Grazul R, Fontes A. Platinum(II) and palladium(II) aryl-thiosemicarbazone complexes: synthesis, characterization, molecular modeling, cytotoxicity, and antimicrobial activity. J COORD CHEM 2014. [DOI: 10.1080/00958972.2014.900664] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- T.T. Tavares
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - D. Paschoal
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - E.V.S. Motta
- Departamento de Bioquímica, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - A.G. Carpanez
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - M.T.P. Lopes
- Departamento de Farmacologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - E.S. Fontes
- Departamento de Bioquímica, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - H.F. Dos Santos
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - H. Silva
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - R.M. Grazul
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - A.P.S. Fontes
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
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26
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Tsipis AC, Karapetsas IN. Accurate prediction of 195Pt NMR chemical shifts for a series of Pt(ii) and Pt(iv) antitumor agents by a non-relativistic DFT computational protocol. Dalton Trans 2014; 43:5409-26. [DOI: 10.1039/c3dt53594k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exhaustive benchmark DFT calculations reveal that the non-relativistic GIAO-PBE0/SARC-ZORA(Pt)∪6-31+G(d)(E) computational protocol predicts accurate 195Pt NMR chemical shifts for a wide range of square planar Pt(ii) and octahedral Pt(iv) anticancer agents.
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Affiliation(s)
- Athanassios C. Tsipis
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- , Greece
| | - Ioannis N. Karapetsas
- Laboratory of Inorganic and General Chemistry
- Department of Chemistry
- University of Ioannina
- , Greece
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27
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Melchior A, Martínez JM, Pappalardo RR, Sánchez Marcos E. Hydration of Cisplatin Studied by an Effective Ab Initio Pair Potential Including Solute–Solvent Polarization. J Chem Theory Comput 2013; 9:4562-73. [DOI: 10.1021/ct400433c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Melchior
- University of Udine, Department of Environmental and
Physical Chemistry, 33100 Udine, Italy
- University of Seville, Department of Physical Chemistry, 41012 Seville, Spain
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28
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Canal Neto A, Jorge F. All-electron double zeta basis sets for the most fifth-row atoms: Application in DFT spectroscopic constant calculations. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.045] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Marques MPM, Valero R, Parker SF, Tomkinson J, Batista de Carvalho LAE. Polymorphism in cisplatin anticancer drug. J Phys Chem B 2013; 117:6421-9. [PMID: 23642237 DOI: 10.1021/jp403486z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study reports a combined experimental and theoretical study of the solid-state polymorphism of the anticancer agent cisplatin. A complete assignment was performed for the inelastic neutron scattering (INS) and Raman spectra collected simultaneously for cisplatin, at different temperatures, with a view to obtain reliable and definitive evidence of the relative thermal stability of its α and β polymorphic species. A marked temperature-dependent hysteresis was observed, as previously reported in the literature. Theoretical calculations were carried out at the density functional theory level, using a plane-wave basis set approach and pseudopotentials. A detailed comparison with the experimental Raman and INS data showed that the α polymorph is present at the lowest temperatures, whereas the β form occurs near room temperature. Furthermore, regions of coexistence of both forms are identified, which depend on the working mode (heating or cooling). These findings imply that Raman spectroscopy allows clear identification of the α and β polymorphs at a given temperature and can unambiguously discriminate between them. Elucidation of the polymorphic equilibrium of this widely used anticancer drug is paramount for its pharmaceutical preparation and storage conditions.
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Affiliation(s)
- M Paula M Marques
- Research Unit Molecular Physical Chemistry, Faculty of Science and Technology, University of Coimbra, 3004-535 Coimbra, Portugal.
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30
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Dos Santos HF, Paschoal D, Burda JV. Exploring the potential energy surface for interaction of a trichloro(diethylenetriamine)gold(III) complex with strong nucleophiles. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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