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Szupryczyński K, Czeleń P, Jeliński T, Szefler B. What is the Reason That the Pharmacological Future of Chemotherapeutics in the Treatment of Lung Cancer Could Be Most Closely Related to Nanostructures? Platinum Drugs in Therapy of Non-Small and Small Cell Lung Cancer and Their Unexpected, Possible Interactions. The Review. Int J Nanomedicine 2024; 19:9503-9547. [PMID: 39296940 PMCID: PMC11410046 DOI: 10.2147/ijn.s469217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/19/2024] [Indexed: 09/21/2024] Open
Abstract
Over the course of several decades, anticancer treatment with chemotherapy drugs for lung cancer has not changed significantly. Unfortunately, this treatment prolongs the patient's life only by a few months, causing many side effects in the human body. It has also been proven that drugs such as Cisplatin, Carboplatin, Oxaliplatin and others can react with other substances containing an aromatic ring in which the nitrogen atom has a free electron group in its structure. Thus, such structures may have a competitive effect on the nucleobases of DNA. Therefore, scientists are looking not only for new drugs, but also for new alternative ways of delivering the drug to the cancer site. Nanotechnology seems to be a great hope in this matter. Creating a new nanomedicine would reduce the dose of the drug to an absolute minimum, and thus limit the toxic effect of the drug; it would allow for the exclusion of interactions with competitive compounds with a structure similar to nucleobases; it would also permit using the so-called targeted treatment and bypassing healthy cells; it would allow for the introduction of other treatment options, such as radiotherapy directly to the cancer site; and it would provide diagnostic possibilities. This article is a review that aims to systematize the knowledge regarding the anticancer treatment of lung cancer, but not only. It shows the clear possibility of interactions of chemotherapeutics with compounds competitive to the nitrogenous bases of DNA. It also shows the possibilities of using nanostructures as potential Platinum drug carriers, and proves that nanomedicine can easily become a new medicinal product in personalized medicine.
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Affiliation(s)
- Kamil Szupryczyński
- Doctoral School of Medical and Health Sciences, Faculty of Pharmacy, Collegium Medicum, Nicolaus, Copernicus University, Bydgoszcz, Poland
| | - Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Tomasz Jeliński
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Beata Szefler
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
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2
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Ondar EE, Polynski MV, Ananikov VP. Predicting 195 Pt NMR Chemical Shifts in Water-Soluble Inorganic/Organometallic Complexes with a Fast and Simple Protocol Combining Semiempirical Modeling and Machine Learning. Chemphyschem 2023:e202200940. [PMID: 36806426 DOI: 10.1002/cphc.202200940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Water-soluble Pt complexes are the key components in medicinal chemistry and catalysis. The well-known cisplatin family of anticancer drugs and industrial hydrosylilation catalysts are two leading examples. On the molecular level, the activity mechanisms of such complexes mostly involve changes in the Pt coordination sphere. Using 195 Pt NMR spectroscopy for operando monitoring would be a valuable tool for uncovering the activity mechanisms; however, reliable approaches for the rapid correlation of Pt complex structure with 195 Pt chemical shifts are very challenging and not available for everyday research practice. While NMR shielding is a response property, molecular 3D structure determines NMR spectra, as widely known, which allows us to build up 3D structure to 195 Pt chemical shift correlations. Accordingly, we present a new workflow for the determination of lowest-energy configurational/conformational isomers based on the GFN2-xTB semiempirical method and prediction of corresponding chemical shifts with a Machine Learning (ML) model tuned for Pt complexes. The workflow was designed for the prediction of 195 Pt chemical shifts of water-soluble Pt(II) and Pt(IV) anionic, neutral, and cationic complexes with halide, NO2 - , (di)amino, and (di)carboxylate ligands with chemical shift values ranging from -6293 to 7090 ppm. The model offered an accuracy (normalized root-mean-square deviation/RMSD) of 1.08 %/145.02 ppm on the held-out test set.
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Affiliation(s)
- Evgeniia E Ondar
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
| | - Mikhail V Polynski
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia.,Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences, 26 Azatutyan Ave, 0014, Yerevan, Armenia
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
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Szefler B, Czeleń P. Will the Interactions of Some Platinum (II)-Based Drugs with B-Vitamins Reduce Their Therapeutic Effect in Cancer Patients? Comparison of Chemotherapeutic Agents such as Cisplatin, Carboplatin and Oxaliplatin-A Review. Int J Mol Sci 2023; 24:ijms24021548. [PMID: 36675064 PMCID: PMC9862491 DOI: 10.3390/ijms24021548] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/04/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Pt (II) derivatives show anti-cancer activity by interacting with nucleobases of DNA, thus causing some spontaneous and non-spontaneous reactions. As a result, mono- and diaqua products are formed which further undergo complexation with guanine or adenine. Consequently, many processes are triggered, which lead to the death of the cancer cell. The theoretical and experimental studies confirm that such types of interactions can also occur with other chemical compounds. The vitamins from B group have a similar structure to the nucleobases of DNA and have aromatic rings with single-pair orbitals. Theoretical and experimental studies were performed to describe the interactions of B vitamins with Pt (II) derivatives such as cisplatin, oxaliplatin and carboplatin. The obtained results were compared with the values for guanine. Two levels of simulations were implemented at the theoretical level, namely, B3LYP/6-31G(d,p) with LANL2DZ bases set for platinum atoms and MN15/def2-TZVP. The polarizable continuum model (IEF-PCM preparation) and water as a solvent were used. UV-Vis spectroscopy was used to describe the drug-nucleobase and drug-B vitamin interactions. Values of the free energy (ΔGr) show spontaneous reactions with mono- and diaqua derivatives of cisplatin and oxaliplatin; however, interactions with diaqua derivatives are more preferable. The strength of these interactions was also compared. Carboplatin products have the weakest interaction with the studied structures. The presence of non-covalent interactions was demonstrated in the tested complexes. A good agreement between theory and experiment was also demonstrated.
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The assessment of physicochemical properties of Cisplatin complexes with purines and vitamins B group. J Mol Graph Model 2022; 113:108144. [DOI: 10.1016/j.jmgm.2022.108144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
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5
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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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Palermo G, Spinello A, Saha A, Magistrato A. Frontiers of metal-coordinating drug design. Expert Opin Drug Discov 2020; 16:497-511. [PMID: 33874825 DOI: 10.1080/17460441.2021.1851188] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: The occurrence of metal ions in biomolecules is required to exert vital cellular functions. Metal-containing biomolecules can be modulated by small-molecule inhibitors targeting their metal-moiety. As well, the discovery of cisplatin ushered the rational discovery of metal-containing-drugs. The use of both drug types exploiting metal-ligand interactions is well established to treat distinct pathologies. Therefore, characterizing and leveraging metal-coordinating drugs is a pivotal, yet challenging, part of medicinal chemistry.Area covered: Atomic-level simulations are increasingly employed to overcome the challenges met by traditional drug-discovery approaches and to complement wet-lab experiments in elucidating the mechanisms of drugs' action. Multiscale simulations, allow deciphering the mechanism of metal-binding inhibitors and metallo-containing-drugs, enabling a reliable description of metal-complexes in their biological environment. In this compendium, the authors review selected applications exploiting the metal-ligand interactions by focusing on understanding the mechanism and design of (i) inhibitors targeting iron and zinc-enzymes, and (ii) ruthenium and gold-based anticancer agents targeting the nucleosome and aquaporin protein, respectively.Expert opinion: The showcased applications exemplify the current role and the potential of atomic-level simulations and reveal how their synergic use with experiments can contribute to uncover fundamental mechanistic facets and exploit metal-ligand interactions in medicinal chemistry.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, United States
| | - Angelo Spinello
- National Research Council (CNR) of Italy, Institute of Material (IOM) @ International School for Advanced Studies (SISSA), Trieste, Italy
| | - Aakash Saha
- Department of Bioengineering, University of California Riverside, Riverside, United States
| | - Alessandra Magistrato
- National Research Council (CNR) of Italy, Institute of Material (IOM) @ International School for Advanced Studies (SISSA), Trieste, Italy
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Szefler B, Czeleń P, Szczepanik A, Cysewski P. Does the Affinity of Cisplatin to B-Vitamins Impair the Therapeutic Effect in the Case of Patients with Lung Cancer-consuming Carrot or Beet Juice? Anticancer Agents Med Chem 2020; 19:1775-1783. [PMID: 30914033 DOI: 10.2174/1871520619666190325150624] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cisplatin (CisPt) has a well-recognized anticancer activity by interacting with DNA and inducing programmed cell death. However, theoretical studies performed on the molecular level suggest that such nonspecific interactions can also take place with many competitive compounds, such as vitamins containing aromatic rings with lone-pair orbitals. OBJECTIVE This work is a theoretical study on the initial Pt-N7(N1) bond formation with vitamins from B group and their comparison with values characterizing native purines. METHODS Geometries of studied structures were optimized with an aid of Gaussian 09 using the B3LYP functional with the 6-31G** basis set. Atomic orbitals of platinum were represented by the lanl2dz basis. Solvation free energies were evaluated by a self-consistent reaction field (SCRF) approach. A dielectric constant of 78 for water was used in the PCM continuum model computations along with radii Bondii. RESULTS The affinities of mono-aqua cis~[Pt(NH3)2Cl(H2O)]+ and di-aqua cis~ [Pt(NH3)2(H2O)2]2+ derivatives of Cisplatinum toward compounds belonging to the group of eight B vitamins were studied and compared to interactions with canonical purines. All the values of ΔGr unambiguously indicate that reactions with cisPt-diaqua are more preferable, but the comparison of ΔGr values obtained for compounds from vitamin B group and the ones characterizing complexes created by Guanine molecules indicates higher affinity of cisPt monomers toward purines. CONCLUSION Based on the observations, the regular intake of vitamin-rich beetroot or carrot juices is strongly discouraged during anticancer therapy using CisPt drug. To confirm the results of the performed computational study, detailed clinical trials should be performed.
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Affiliation(s)
- Beata Szefler
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096, Bydgoszcz, Poland
| | - Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096, Bydgoszcz, Poland
| | - Adam Szczepanik
- The Kuyavian and Pomeranian Pulmonology Centre in Bydgoszcz Lung Cancer Treatment Department, Seminaryjna 1, 84-326, Bydgoszcz, Poland
| | - Piotr Cysewski
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096, Bydgoszcz, Poland
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8
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Janoš P, Spinello A, Magistrato A. All-atom simulations to studying metallodrugs/target interactions. Curr Opin Chem Biol 2020; 61:1-8. [PMID: 32781390 DOI: 10.1016/j.cbpa.2020.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/03/2020] [Accepted: 07/12/2020] [Indexed: 12/16/2022]
Abstract
Metallodrugs are extensively used to treat and diagnose distinct disease types. The unique physical-chemical properties of metal ions offer tantalizing opportunities to tailor effective scaffolds for selectively targeting specific biomolecules. Modern experimental techniques have collected a large body of structural data concerning the interactions of metallodrugs with their biomolecular targets, although being unable to exhaustively assess the molecular basis of their mechanism of action. In this scenario, the complementary use of accurate computational methods allows uncovering the minutiae of metallodrugs/targets interactions and their underlying mechanism of action at an atomic-level of detail. This knowledge is increasingly perceived as an invaluable requirement to rationally devise novel and selective metallodrugs. Building on literature studies, selected largely from the last 2 years, this compendium encompasses a cross-section of the current role, advances, and challenges met by computer simulations to decipher the mechanistic intricacies of prototypical metallodrugs.
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Affiliation(s)
- Pavel Janoš
- CNR-IOM c/o SISSA, Via Bonomea 265, 34136, Trieste, Italy
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9
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Alshammari N, Platts JA. Theoretical study of copper binding to GHK peptide. Comput Biol Chem 2020; 86:107265. [PMID: 32371360 DOI: 10.1016/j.compbiolchem.2020.107265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/20/2022]
Abstract
We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xTB semi-empirical and B3LYP-D DFT levels. Conventional molecular dynamics simulation of Cu-GHK shows the stability of the copper-peptide binding over 100 ps trajectory. Four equatorial bonds in 3N1O coordination remain stable throughout simulation, while a fifth in apical position from C-terminal carboxylate is more fluxional. We also show that the automated conformer and rotamer search algorithm CREST is able to correctly predict the metal binding position from a starting point consisting of separated peptide, copper and water.
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Affiliation(s)
- Nadiyah Alshammari
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK.
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10
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Kuang G, Murugan NA, Ågren H. Mechanistic Insight into the Binding Profile of DCVJ and α-Synuclein Fibril Revealed by Multiscale Simulations. ACS Chem Neurosci 2019; 10:610-617. [PMID: 30277753 DOI: 10.1021/acschemneuro.8b00465] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Parkinson's disease (PD) is a serious neurodegenerative disease and is characterized by abnormal α-synuclein (α-syn) accumulation in Lewy bodies (LB) and Lewy neurites (LN), which makes α-syn an important imaging target for PD. An imaging probe that quantifies fibrillar α-syn can enhance the clinical diagnosis of PD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the α-syn fibril in the brain. In this paper, we study the binding profile of fibrillar α-syn with a fluorescent probe 4-(dicyanovinyl)julolidine (DCVJ), which is being explored for identifying α-syn imaging agents. A multiscale simulation workflow including molecular docking, molecular dynamics, metadynamics, and QM/MM calculations was implemented. We find that DCVJ can bind to multiple sites of α-syn which are located either at the surface or in the core. Free energy calculations using implicit solvent models reveal that the most favorable binding mode for DCVJ is associated with the core binding site and is further confirmed by metadyamics simulation. Besides, a dynamic binding pathway is discovered, which reveals that DCVJ binds gradually into the core of the fibril passing through several intermediate states. The conformational arrest of the dicyano vinyl group in the fibrillar environment could explain the reason behind the fibril-specific fluorescence of DCVJ. Furthermore, based on hybrid QM/MM calculations, the molecular geometry of the dicyano vinyl group is found to be environment specific which explains why DCVJ serves as a staining agent for such fibrillar-like environments. Our results could be helpful for elucidating the binding mechanism of imaging tracers with the fibrillar form of α-syn and explain their fibrillar-specific optical properties, a knowledge that in turn can be used to guide the design and development of compounds with higher affinity and selectivity for α-syn using structure-based strategies.
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Affiliation(s)
- Guanglin Kuang
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan, 475004P. R. China
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Synthesis, spectroscopic characterization and in vitro cytotoxic as well as docking studies of cis-diammine platinum(II) complexes of thiones. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.09.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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12
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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14
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Srivastava R. Theoretical studies on the electronic and optoelectronic properties of [A.2AP(w)/A*.2AP(WC)/C.2AP(w)/C*.2AP(WC)/C.A(w)/C*.A(WC)]–Au8 mismatch nucleobase complexes. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1382737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ruby Srivastava
- Center for Molecular Modeling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
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15
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Dehez F, Gattuso H, Bignon E, Morell C, Dumont E, Monari A. Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates. Nucleic Acids Res 2017; 45:3654-3662. [PMID: 28334906 PMCID: PMC5397166 DOI: 10.1093/nar/gkx148] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/21/2017] [Indexed: 02/01/2023] Open
Abstract
DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 μs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.
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Affiliation(s)
- François Dehez
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana Champaign
| | - Hugo Gattuso
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
| | - Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France.,Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Antonio Monari
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
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16
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Spinello A, Magistrato A. An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era. Expert Opin Drug Discov 2017; 12:813-825. [DOI: 10.1080/17460441.2017.1340272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
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17
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Díaz-Gómez DG, Galindo-Murillo R, Cortés-Guzmán F. The Role of the DNA Backbone in Minor-Groove Ligand Binding. Chemphyschem 2017; 18:1909-1915. [PMID: 28463411 DOI: 10.1002/cphc.201700260] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/08/2022]
Abstract
Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.
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Affiliation(s)
- Dalia G Díaz-Gómez
- Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Col. Copilco Bajo, 4510, Mexico, Mexico
| | | | - Fernando Cortés-Guzmán
- Instituto de Quimica, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, Col. Copilco Bajo, 4510, Mexico, Mexico
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18
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de Cózar A, Larrañaga O, Bickelhaupt FM, San Sebastián E, Ortega-Carrasco E, Maréchal JD, Lledós A, Cossío FP. New Insights into the Reactivity of Cisplatin with Free and Restrained Nucleophiles: Microsolvation Effects and Base Selectivity in Cisplatin-DNA Interactions. Chemphyschem 2016; 17:3932-3947. [DOI: 10.1002/cphc.201600982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Abel de Cózar
- Departamento de Química Orgánica I and ORFEO-CINQA, Kimika Organikoa I Saila, Facultad de Química/Kimika Fakultatea; Universidad del País Vasco, Euskal Herriko Unibertsitatea UPV/EH and Donostia International Physics Center (DIPC); P. K. 1072 20018 San Sebastián-Donostia Spain
- IKERBASQUE, Basque Foundation for Science; 48011 Bilbao Spain
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); VU University Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Olatz Larrañaga
- Departamento de Química Orgánica I and ORFEO-CINQA, Kimika Organikoa I Saila, Facultad de Química/Kimika Fakultatea; Universidad del País Vasco, Euskal Herriko Unibertsitatea UPV/EH and Donostia International Physics Center (DIPC); P. K. 1072 20018 San Sebastián-Donostia Spain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); VU University Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University Nijmegen; Heyendaalseweg 135 NL-6525 AJ Nijmegen The Netherlands
| | - Eider San Sebastián
- Dept. Química Aplicada, Química Inorgánica, Facultad de Química/ Kimika Fakultatea; Universidad del País Vasco, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3; 20018 San Sebastián-Donostia Spain
| | | | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Agustí Lledós
- Departament de Química; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Fernando P. Cossío
- Departamento de Química Orgánica I and ORFEO-CINQA, Kimika Organikoa I Saila, Facultad de Química/Kimika Fakultatea; Universidad del País Vasco, Euskal Herriko Unibertsitatea UPV/EH and Donostia International Physics Center (DIPC); P. K. 1072 20018 San Sebastián-Donostia Spain
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19
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Jalili S, Maddah M, Schofield J. Molecular dynamics simulation and free energy analysis of the interaction of platinum-based anti-cancer drugs with DNA. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cisplatin and oxaliplatin are two widely-used anti-cancer drugs which covalently bind to a same location in DNA strands. Platinum agents make intrastrand and interstrand cross-links with the N7 atoms of guanine nucleotides which prevent DNA from polymerization by causing a distortion in the double helix. Molecular dynamics simulations and free energy calculations were carried out to investigate the binding of two platinum-based anti-cancer drugs with DNA. We compared the binding of these drugs which differ in their carrier ligands, and hence their potential interactions with DNA. When a platinum agent binds to nucleotides, it causes a high amount of deformation in DNA structure. To find the extent of deformation, torsion angles and base pair and groove parameters of DNA were considered. These parameters were compared with normal B-DNA which was considered as the undamaged DNA. The formation of hydrogen bonds between drugs and DNA nucleotides was examined in solution. It was shown that oxaliplatin forms more hydrogen bonds than cisplatin. Our results confirm that the structure of the platinated DNA rearranges significantly and cisplatin tries to deform DNA more than oxaliplatin. The binding free energies were also investigated to understand the affinities, types and the contributions of interactions between drugs and DNA. It was concluded that oxaliplatin tendency for binding to DNA is more than cisplatin in solvent environment. The binding free energy was calculated based on the MM/PBSA and MM/GBSA methods and the results of QM/MM calculations verified them.
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Affiliation(s)
- Seifollah Jalili
- Department of Chemistry, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran
- Computational Physical Sciences Research Laboratory, School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), P. O. Box 19395-5531 Tehran, Iran
| | - Mina Maddah
- Department of Chemistry, K. N. Toosi University of Technology, P. O. Box 15875-4416, Tehran, Iran
| | - Jeremy Schofield
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Ontario M5S 3H6, Canada
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Zábojníková T, Cajzl R, Kljun J, Chval Z, Turel I, Burda JV. Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study. J Comput Chem 2016; 37:1766-80. [PMID: 27185047 DOI: 10.1002/jcc.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half-sandwich complexes were performed in water environment using the B3PW91/6-31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single-point (SP) calculations were performed at the B3LYP/6-311++G(2df,2pd)/DPCM/saled-UAKS level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tereza Zábojníková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Radim Cajzl
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, České Budějovice, 370 11, Czech Republic
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - 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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21
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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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22
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Nechay MR, Valdez CE, Alexandrova AN. Computational Treatment of Metalloproteins. J Phys Chem B 2015; 119:5945-56. [DOI: 10.1021/acs.jpcb.5b00028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michael R. Nechay
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Crystal E. Valdez
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anastassia N. Alexandrova
- Department
of Chemistry and Biochemistry and ‡California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
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23
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Combining anti-cancer drugs with artificial sweeteners: Synthesis and anti-cancer activity of saccharinate (sac) and thiosaccharinate (tsac) complexes cis -[Pt(sac) 2 (NH 3 ) 2 ] and cis -[Pt(tsac) 2 (NH 3 ) 2 ]. J Inorg Biochem 2014; 141:55-57. [DOI: 10.1016/j.jinorgbio.2014.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 02/05/2023]
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24
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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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25
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Sarmah A, Roy RK. A density functional reactivity theory (DFRT) based approach to understand the interaction of cisplatin analogues with protecting agents. J Comput Aided Mol Des 2014; 28:1153-73. [DOI: 10.1007/s10822-014-9790-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/23/2014] [Indexed: 01/24/2023]
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26
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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27
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Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules 2014; 4:616-45. [PMID: 25006697 PMCID: PMC4192665 DOI: 10.3390/biom4030616] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/16/2022] Open
Abstract
Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.
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Affiliation(s)
- Pietro Vidossich
- Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain.
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy.
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28
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Murugan NA. Solvatochromism in a Pyridinium Cyclopentadienylide: Insights from a Sequential Car–Parrinello QM/MM and TD-DFT/Semicontinuum Approach. J Phys Chem B 2014; 118:7358-66. [DOI: 10.1021/jp410854b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- N. Arul Murugan
- Division of Theoretical Chemistry
and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691, Stockholm, Sweden
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29
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Kumbhar S, Johannsen S, Sigel RK, Waller MP, Müller J. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs. J Inorg Biochem 2013; 127:203-10. [DOI: 10.1016/j.jinorgbio.2013.03.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/18/2013] [Accepted: 03/18/2013] [Indexed: 01/04/2023]
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30
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Theoretic study of DNA base guanine and adenine and protein residues’ binding mode of the trans geometries of new antitumor non-classical platinum complexes containing pyridine and picoline ligand. Struct Chem 2013. [DOI: 10.1007/s11224-013-0204-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Can the chemical reactivity of an ultimate carcinogen be related to its carcinogenicity? An application to propylene oxide. Toxicol In Vitro 2013; 27:479-85. [DOI: 10.1016/j.tiv.2012.07.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/27/2012] [Accepted: 07/30/2012] [Indexed: 11/21/2022]
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32
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Gkionis K, Mutter ST, Platts JA. QM/MM description of platinum–DNA interactions: comparison of binding and DNA distortion of five drugs. RSC Adv 2013. [DOI: 10.1039/c3ra23041d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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33
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Pauwels E, Claeys D, Martins JC, Waroquier M, Bifulco G, Speybroeck VV, Madder A. Accurate prediction of 1H chemical shifts in interstrand cross-linked DNA. RSC Adv 2013. [DOI: 10.1039/c3ra22408b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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34
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Sarmah A, Roy RK. Understanding the preferential binding interaction of aqua-cisplatins with nucleobase guanine over adenine: a density functional reactivity theory based approach. RSC Adv 2013. [DOI: 10.1039/c2ra23223e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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35
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Ortega-Carrasco E, Cossío FP, Lledós A, Maréchal JD. Computational insights on the possibility of tri-coordinated cisplatinated adducts with protein models. J Inorg Biochem 2012; 117:230-6. [DOI: 10.1016/j.jinorgbio.2012.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 11/30/2022]
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36
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Elder RM, Jayaraman A. Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.654208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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37
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Nguyen TH, Arnesano F, Scintilla S, Rossetti G, Ippoliti E, Carloni P, Natile G. Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. J Chem Theory Comput 2012; 8:2912-20. [DOI: 10.1021/ct300167m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Trung Hai Nguyen
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Fabio Arnesano
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Simone Scintilla
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, D-52425 Jülich, Germany,
and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Statistical and Biological Physics Sector, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265,
I-34136 Trieste, Italy
| | - Giovanni Natile
- Department Farmaco-Chimico, University of Bari “A. Moro”, via Edoardo
Orabona 4, 70125 Bari, Italy
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38
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Tai HC, Brodbeck R, Kasparkova J, Farrer NJ, Brabec V, Sadler PJ, Deeth RJ. Combined Theoretical and Computational Study of Interstrand DNA Guanine–Guanine Cross-Linking by trans-[Pt(pyridine)2] Derived from the Photoactivated Prodrug trans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]. Inorg Chem 2012; 51:6830-41. [DOI: 10.1021/ic3005745] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hui-Chung Tai
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Ralf Brodbeck
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Jana Kasparkova
- The Institute of
Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 61265 Brno, Czech Republic
| | - Nicola J. Farrer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Viktor Brabec
- The Institute of
Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 61265 Brno, Czech Republic
| | - Peter J. Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
| | - Robert J. Deeth
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United
Kingdom
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39
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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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40
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Istrate AN, Tsvetkov PO, Mantsyzov AB, Kulikova AA, Kozin SA, Makarov AA, Polshakov VI. NMR solution structure of rat aβ(1-16): toward understanding the mechanism of rats' resistance to Alzheimer's disease. Biophys J 2012; 102:136-43. [PMID: 22225807 DOI: 10.1016/j.bpj.2011.11.4006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/15/2011] [Accepted: 11/23/2011] [Indexed: 11/26/2022] Open
Abstract
In an attempt to reveal the mechanism of rats' resistance to Alzheimer's disease, we determined the structure of the metal-binding domain 1-16 of rat β-amyloid (rat Aβ(1-16)) in solution in the absence and presence of zinc ions. A zinc-induced dimerization of the domain was detected. The zinc coordination site was found to involve residues His-6 and His-14 of both peptide chains. We used experimental restraints obtained from analyses of NMR and isothermal titration calorimetry data to perform structure calculations. The calculations employed an explicit water environment and a simulated annealing molecular-dynamics protocol followed by quantum-mechanical/molecular-mechanical optimization. We found that the C-tails of the two polypeptide chains of the rat Aβ(1-16) dimer are oriented in opposite directions to each other, which hinders the assembly of rat Aβ dimers into oligomeric aggregates. Thus, the differences in the structure of zinc-binding sites of human and rat Aβ(1-16), their ability to form regular cross-monomer bonds, and the orientation of their hydrophobic C-tails could be responsible for the resistance of rats to Alzheimer's disease.
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Affiliation(s)
- Andrey N Istrate
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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41
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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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42
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Alberto ME, Butera V, Russo N. Which One among the Pt-Containing Anticancer Drugs More Easily Forms Monoadducts with G and A DNA Bases? A Comparative Study among Oxaliplatin, Nedaplatin, and Carboplatin. Inorg Chem 2011; 50:6965-71. [DOI: 10.1021/ic200148n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Chval Z, Futera Z, Burda JV. Comparison of hydration reactions for “piano-stool” RAPTA-B and [Ru(η6− arene)(en)Cl]+ complexes: Density functional theory computational study. J Chem Phys 2011; 134:024520. [DOI: 10.1063/1.3515534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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45
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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46
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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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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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48
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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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Lau JKC, Ensing B. Hydrolysis of cisplatin—a first-principles metadynamics study. Phys Chem Chem Phys 2010; 12:10348-55. [DOI: 10.1039/b918301a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Futera Z, Klenko J, Šponer JE, Šponer J, Burda JV. Interactions of the “piano-stool” [ruthenium(II) (η6-arene)(en)CL]+complexes with water and nucleobases; ab initio and DFT study. J Comput Chem 2009; 30:1758-70. [DOI: 10.1002/jcc.21179] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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