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Formation of bifunctional cross-linked products due to reaction of NAMI-A with DNA bases – a DFT study. Struct Chem 2022. [DOI: 10.1007/s11224-022-01897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Šebesta F, Šebera J, Sychrovský V, Tanaka Y, Burda JV. QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH. J Comput Chem 2020; 41:1509-1520. [PMID: 32208552 DOI: 10.1002/jcc.26194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023]
Abstract
The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg2+ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H2 O)6 ]2+ , (2) T + [Hg(H2 O)5 (OH)]+ , (3) T + Hg(H2 O)4 (OH)2 , and (4) N3-deprotonated T + Hg(H2 O)4 (OH)2 . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg2+ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Japan
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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Cerón-Carrasco JP, Zúñiga J, Requena A. Tuning the Optical Properties of Novel Antitumoral Drugs Based on Cyclometalated Iridium(III) Complexes. J Phys Chem A 2019; 123:8644-8649. [PMID: 31536343 DOI: 10.1021/acs.jpca.9b06216] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most of the current efforts in drug discovery are devoted to the design of molecules able to mitigate side effects by concentrating the biological action in the targeted tissue. One promising strategy is photodynamic therapy, which is based on the in situ generation of reactive singlet oxygen upon radiation exposure. However, such an approach requires the use of an efficient photosensitizer. This contribution deals with the optical properties of an Ir(III) complex, [Ir(pbz)2(N^N)] (pbz = 2-phenylbenzimidazole; N^N = methyl 1-butyl-2-pyridyl-benzimidazole-5-carboxylate), which has recently been shown to exhort a strong photoactivity, but still needs further improvements to reach clinical applications. We performed density functional theory calculations at the M06, PBE0, ωB97xD, and CAM-B3LYP levels to predict the impact of introducing electron donor-acceptor groups into the nature of the lowest excited states. The simulations performed demonstrate that the presence of a NH2 at the pbz ligand and a NO2 group at the N^N ligand yield a bathochromic shift of absorption spectrum. We report the most sensitive positions to tune the optical signatures of this family of complexes.
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Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics and High Performance Computing Research Group (BIO-HPC) Universidad Católica San Antonio de Murcia (UCAM) Campus de los Jerónimos , 30107 , Murcia , Spain and
| | - José Zúñiga
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
| | - Alberto Requena
- Departamento de Química Física , Universidad de Murcia , 30100 Murcia , Spain
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Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes. J Mol Model 2018; 24:98. [DOI: 10.1007/s00894-018-3598-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 12/11/2022]
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Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study. J Biol Inorg Chem 2018; 23:363-376. [DOI: 10.1007/s00775-018-1536-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 02/01/2023]
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Cerón-Carrasco JP, Ruiz J, Vicente C, de Haro C, Bautista D, Zúñiga J, Requena A. DFT Simulation of Structural and Optical Properties of 9-Aminoacridine Half-Sandwich Ru(II), Rh(III), and Ir(III) Antitumoral Complexes and Their Interaction with DNA. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00139] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics
and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Campus de los
Jerónimos, 30107 Murcia, Spain
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Aradhyula BPR, Kalidasan M, Gangele K, Deb DK, Shepherd SL, Phillips RM, Poluri KM, Kollipara MR. Synthesis, Structural and Biological Studies of Some Half-Sandwich d6-Metal Complexes with Pyrimidine-Based Ligands. ChemistrySelect 2017. [DOI: 10.1002/slct.201601926] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Mahesh Kalidasan
- Centre for Advanced Studies in Chemistry; North-Eastern Hill University; Shillong- 793 022 India
| | - Krishnakant Gangele
- Department of Biotechnology and Center for Nanotechnology; Indian Institute of Technology Roorkee; Roorkee- 247667, Uttarakhand India
| | - Debojit K. Deb
- Centre for Advanced Studies in Chemistry; North-Eastern Hill University; Shillong- 793 022 India
| | - Samanta L. Shepherd
- Department of Pharmacy; School of Applied Sciences; University of Huddersfield; Huddersfield - HD1 3DH UK
| | - Roger M. Phillips
- Department of Pharmacy; School of Applied Sciences; University of Huddersfield; Huddersfield - HD1 3DH UK
| | - Krishna Mohan Poluri
- Department of Biotechnology and Center for Nanotechnology; Indian Institute of Technology Roorkee; Roorkee- 247667, Uttarakhand India
| | - Mohan Rao Kollipara
- Centre for Advanced Studies in Chemistry; North-Eastern Hill University; Shillong- 793 022 India
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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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Singh AK, Saxena G, Dixit S, Hamidullah, Singh SK, Singh SK, Arshad M, Konwar R. Synthesis, characterization and biological activities of some Ru(II) complexes with substituted chalcones and their applications as chemotherapeutics against breast cancer. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.01.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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Das D, Mondal P. Interaction of ruthenium(ii) antitumor complexes with d(ATATAT)2 and d(GCGCGC)2: a theoretical study. NEW J CHEM 2015. [DOI: 10.1039/c4nj02118e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the interaction of three ruthenium(ii) complexes with d(ATATAT)2 and d(GCGCGC)2 sequences by using the molecular docking and quantum mechanics/molecular mechanics (QM/MM) hybrid method.
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Affiliation(s)
- Dharitri Das
- Department of Chemistry
- Assam University
- Silchar 788011
- India
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Cerón-Carrasco JP, Cerezo J, Requena A, Zuñiga J, Contreras-García J, Chavan S, Manrubia-Cobo M, Pérez-Sánchez H. Labelling Herceptin with a novel oxaliplatin derivative: a computational approach towards the selective drug delivery. J Mol Model 2014; 20:2401. [PMID: 25149438 DOI: 10.1007/s00894-014-2401-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
Abstract
The clinical use of platinum(II)-based drugs has serious side effects due to the non-specific reactions with both malignant and normal cells. To circumvent such major drawback, novel metallodrugs might be combined with suitable carrier molecules, as antibodies, to ensure selective attacks on tumours while sparing healthy tissues. In this contribution, we investigate the stability of a novel oxaliplatin derivate drug embedded in Herceptin (trastuzumab), an antibody which is able to recognise breast cancer cells, by using a wide panel of theoretical tools: docking, molecular dynamics and quantum calculations. Our calculations reveal the binding mechanism: the drug initially interacts non-covalently with the Pro40A and Asp167A residues, and the nitrogen of His171B subsequently replaces one of the water molecules coordinated to the platinum center, where the latter step reversibly fixes the drug into the antibody. These data might be used to further rationalise the synthesis of improved drugs beyond classical platinum(II) derivatives by improving the ligand-protein coupling mode.
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Affiliation(s)
- José P Cerón-Carrasco
- Departamento de Química Física, Facultad de Química, Universidad de Murcia, 30100 Campus de Espinardo, Murcia, Spain,
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Futera Z, Burda JV. Reaction mechanism of Ru(II) piano‐stool complexes: Umbrella sampling QM/MM MD study. J Comput Chem 2014; 35:1446-56. [DOI: 10.1002/jcc.23639] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/23/2014] [Accepted: 05/02/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Zdeněk Futera
- Department of ChemistryFaculty of Science and TechnologyKeio University, 3‐14‐1 HiyoshiKohoku‐ku Yokohama223‐8522 Japan
| | - Jaroslav V. Burda
- Faculty of Mathematics and PhysicsCharles University in PragueKe Karlovu 3, 121 16 Prague 2 Czech Republic
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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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