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Santos TMR, Tavares CA, da Cunha EFF, Ramalho TC. Vanadium complex as a potential modulator of the autophagic mechanism through proteins PI3K and ULK1: development, validation and biological implications of a specific force field for [VO(bpy) 2Cl]. J Biomol Struct Dyn 2024; 42:9118-9132. [PMID: 37608540 DOI: 10.1080/07391102.2023.2250453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023]
Abstract
The modulation of autophagy has been presented as a very useful strategy in anticancer treatments. In this sense, the vanadium complex (VC) bis(2,2'-bipyridine)chlorooxovanadium(IV), [VO(bpy)2Cl], is known for its ability to induce autophagy in triple-negative breast cancer cells (TNBC). An excellent resource to investigate the role of VC in the induction of autophagy is to make use of Molecular Dynamics (MD) simulations. However, until now, the scarcity of force field parameters for the VC prevented a reliable analysis. The autophagy signaling pathway starts with the PI3K protein and ends with ULK1. Therefore, in the first stage of this work, we developed a new AMBER force field for the VC (VCFF) from a quantum structure, obtained by DFT calculations. In the second stage, the VCFF was validated through structural analyses. From this, it was possible to investigate, through docking and MD (200 ns), the performance of the PI3K-VC and ULK1-VC systems (third stage). The analyses of this last stage involved RMSD, hydrogen bonds, RMSF and two pathways for the modulation of autophagy. In general, this work fills in the absence of force field parameters (FF) for VC by proposing an efficient and new FF, in addition to investigating, at the molecular level, how VC is able to induce autophagy in TNBC cells. This study encourages new parameterizations of metallic complexes and contributes to the understanding of the duality of autophagic processes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, Brazil
| | - Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
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2
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Vavrečka A, Fatková K, Burda JV. Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data. J Comput Chem 2024; 45:1727-1736. [PMID: 38595085 DOI: 10.1002/jcc.27361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 04/11/2024]
Abstract
This study compares results of four relativistic pseudopotential basis sets, which differ mainly by their size: double-zeta introduced by Hay and Wadt from Los Alamos National Laboratory (LANL2DZ), triple-zeta based on Stuttgart energy-consistent scalar-relativistic pseudopotential (SDD3), its extension with 2fg polarization functions, and combination of Stuttgart pseudopotentials with quintuple-zeta cc-pV5Z base (SDD5). Hydrides of transition metals from Cr to Zn group are chosen as reference molecules. The coupled cluster method (CCSD(T)) is used for evaluation of selected molecular characteristics. Interatomic distances, dissociation energies, vibration modes, and anharmonicity constants are determined and compared with available experimental data. As expected, the accuracy of basis depends mainly on its size. However, only moderate modification of SDD3 basis set significantly improves its accuracy, which becomes comparable to the largest basis set. Nevertheless, the time consumption is significantly lower.
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Affiliation(s)
- Adam Vavrečka
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Kateřina Fatková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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3
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Zhang T, Li X, Wu L, Su Y, Yang J, Zhu X, Li G. Enhanced cisplatin chemotherapy sensitivity by self-assembled nanoparticles with Olaparib. Front Bioeng Biotechnol 2024; 12:1364975. [PMID: 38415186 PMCID: PMC10898354 DOI: 10.3389/fbioe.2024.1364975] [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: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Abstract
Cisplatin (CDDP) is widely used as one kind of chemotherapy drugs in cancer treatment. It functions by interacting with DNA, leading to the DNA damage and subsequent cellular apoptosis. However, the presence of intracellular PARP1 diminishes the anticancer efficacy of CDDP by repairing DNA strands. Olaparib (OLA), a PARP inhibitor, enhances the accumulation of DNA damage by inhibiting its repair. Therefore, the combination of these two drugs enhances the sensitivity of CDDP chemotherapy, leading to improved therapeutic outcomes. Nevertheless, both drugs suffer from poor water solubility and limited tumor targeting capabilities. To address this challenge, we proposed the self-assembly of two drugs, CDDP and OLA, through hydrogen bonding to form stable and uniform nanoparticles. Self-assembled nanoparticles efficiently target tumor cells and selectively release CDDP and OLA within the acidic tumor microenvironment, capitalizing on their respective mechanisms of action for improved anticancer therapy. In vitro studies demonstrated that the CDDP-OLA NPs are significantly more effective than CDDP/OLA mixture and CDDP at penetrating cancer cells and suppressing their growth. In vivo studies revealed that the nanoparticles specifically accumulated at the tumor site and enhanced the therapeutic efficacy without obvious adverse effects. This approach holds great potential for enhancing the drugs' water solubility, tumor targeting, bioavailability, and synergistic anticancer effects while minimizing its toxic side effects.
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Affiliation(s)
- Tao Zhang
- Key Laboratory of Microecology-immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi, China
| | - Xiao Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liang Wu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Su
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Jiapei Yang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, China
| | - Guolin Li
- Key Laboratory of Microecology-immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi, China
- Department of Oral, Shanghai Eighth People’s Hospital, Xuhui Branch of Shanghai Sixth People’s Hospital, Shanghai, China
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Chen X, Vo T, Clancy P. A multiscale approach to uncover the self-assembly of ligand-covered palladium nanocubes. SOFT MATTER 2023; 19:8625-8634. [PMID: 37916973 DOI: 10.1039/d3sm01140b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Ligand-mediated superlattice assemblies of metallic nanocrystals represent a new type of mesoscale materials whose structural ordering directly influence emergent collective properties. However, universal control over the spatial and orientational ordering of their constitutive components remains an open challenge. One major barrier contributing to the lack of programmability in these nanoscale building blocks revolves around a gap in fundamental understanding of how ligand-mediated interactions at the particle level propagate to macroscopic and mesoscale behaviors. Here, we employ a combination of scaling theory and coarse-grained simulations to develop a multiscale modeling framework capable of bridging across hierarchical assembly length scales for a model system of ligand-functionalized nanocubes (here, Pd). We first employ atomistic simulations to characterize how specific ligand-ligand interactions influence the local behaviors between neighboring Pd nanocubes. We then utilize a mean-field scaling theory to both rationalize the observed behaviors as well as compute a coarse-grained effective pairwise potential between nanocubes capable of reproducing atomistic behaviors at the mesoscale. Furthermore, our simulations reveal that a complex interplay between ligand-ligand interactions is directly responsible for a shift in macroscopic ordering between neighboring nanocubes. Our results, therefore, provides a critical step forward in establishing a multiscale understanding of ligand-functionalized nanocrystalline assemblies that can be subsequently leveraged to design targeted structures exhibiting novel, emergent collective properties.
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Affiliation(s)
- Xiangyu Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Thi Vo
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
| | - Paulette Clancy
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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Franco LR, Toledo KCF, Matias TA, Araujo CM, Araki K, Coutinho K. Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution. Phys Chem Chem Phys 2023; 25:24475-24494. [PMID: 37655780 DOI: 10.1039/d3cp02154h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2'-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.
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Affiliation(s)
- Leandro Rezende Franco
- Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, 05508-090 Sao Paulo, SP, Brazil
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.
| | | | - Tiago Araujo Matias
- Instituto de Quimica, Universidade de Sao Paulo, Av. Lineu Prestes 748, Butanta, 05508-000 Sao Paulo, SP, Brazil
| | - C Moyses Araujo
- Department of Engineering and Physics, Karlstad University, 65188 Karlstad, Sweden.
- Materials Theory Division, Department of Physics and Astronomy, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Koiti Araki
- Instituto de Quimica, Universidade de Sao Paulo, Av. Lineu Prestes 748, Butanta, 05508-000 Sao Paulo, SP, Brazil
| | - Kaline Coutinho
- Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, 05508-090 Sao Paulo, SP, Brazil
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Tavares CA, Santos TMR, da Cunha EFF, Ramalho TC. Parameterization and validation of a new AMBER force field for an oxovanadium (IV) complex with therapeutic potential implications in Alzheimer's disease. J Mol Graph Model 2023; 122:108511. [PMID: 37167701 DOI: 10.1016/j.jmgm.2023.108511] [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: 12/21/2022] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
The scarcity of efficient force fields to describe metal complexes may be a problem for new advances in medicinal chemistry. Thus, the development of force fields for these compounds can be valuable for the scientific community, especially when it comes to molecules that show interesting outputs regarding potential treating of diseases. Vanadium complexes, for instance, have shown promising results towards therapeutics of Alzheimer's Disease, most notably the bis(maltolato)oxovanadium (IV). Therefore, the mainly goal of this work is to develop and validate a new set of parameters for this vanadium complex from a minimum energy structure, obtained by DFT calculations, where great results of the new force field are found when confronted with experimental and quantum reference values. Moreover, the new force field showed to be quite effective to describe the molecule of under study whilst GAFF could not describe it effectively. In addition, a case study points out hydrogen bonds in the vanadium complex-PTP1B system.
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Affiliation(s)
- Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200-000, Brazil; Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, 500 03, Czech Republic.
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7
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Santos TMR, Tavares CA, Pereira AF, da Cunha EFF, Ramalho TC. Evaluation of autophagy inhibition to combat cancer: (vanadium complex)-protein interactions, parameterization, and validation of a new force field. J Mol Model 2023; 29:123. [PMID: 36995564 PMCID: PMC10061415 DOI: 10.1007/s00894-023-05530-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
Autophagy has drawn attention from the scientific community, mainly because of its significant advantages over chemotherapeutic processes. One of these advantages is its direct action on cancer cells, avoiding possible side effects, unlike chemotherapy, which reaches tumor cells and affects healthy cells in the body, leading to a great loss in the quality of life of patients. In this way, it is known that vanadium complex (VC) [VO(oda)(phen)] has proven inhibition effect on autophagy process in pancreatic cancer cells. Keeping that in mind, molecular dynamics (MD) simulations can be considered excellent strategies to investigate the interaction of metal complexes and their biological targets. However, simulations of this type are strongly dependent on the appropriate choice of force field (FF). Therefore, this work proposes the development of AMBER FF parameters for VC, having a minimum energy structure as a starting point, obtained through DFT calculations with B3LYP/def2-TZVP level of theory plus ECP for the vanadium atom. An MD simulation in vacuum was performed to validate the developed FF. From the structural analyses, satisfying values of VC bond lengths and angles were obtained, where a good agreement with the experimental data and the quantum reference was found. The RMSD analysis showed an average of only 0.3%. Finally, we performed docking and MD (120 ns) simulations with explicit solvent between VC and PI3K. Overall, our findings encourage new parameterizations of metal complexes with significant biological applications, as well as allow to contribute to the elucidation of the complex process of autophagy.
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Affiliation(s)
- Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil.
| | - Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil
| | - Ander F Pereira
- Institute of Chemistry, University of Campinas, /SP, Campinas, 13083-970, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, /MG, Lavras, 37200-000, Brazil.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
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8
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Tavares CA, Santos TMR, da Cunha EFF, Ramalho TC. Molecular Dynamics-Assisted Interaction of Vanadium Complex-AMPK: From Force Field Development to Biological Application for Alzheimer's Treatment. J Phys Chem B 2023; 127:495-504. [PMID: 36603208 DOI: 10.1021/acs.jpcb.2c07147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A large part of the world's population is affected by Alzheimer's disease (AD) and diabetes mellitus type 2, which cause both social and economic impacts. These two conditions are associated with one protein, AMPK. Studies have shown that vanadium complexes, such as bis(N',N'-dimethylbiguanidato)-oxovanadium(IV), VO(metf)2·H2O, are potential agents against AD. A crucial step in drug design studies is obtaining information about the structure and interaction of these complexes with the biological targets involved in the process through molecular dynamics (MD) simulations. However, MD simulations depend on the choice of a good force field that could present reliable results. Moreover, general force fields are not efficient for describing the properties of metal complexes, and a VO(metf)2·H2O-specific force field does not yet exist; thus, the proper development of a parameter set is necessary. Furthermore, this investigation is essential and relevant given the importance for both the scientific community and the population that is affected by this neurodegenerative disease. Therefore, the present work aims to develop and validate the AMBER force field parameters for VO(metf)2·H2O since the literature lacks such information on metal complexes and investigate through classical molecular dynamics the interactions made by the complex with the protein. The proposed force field proved to be effective for describing the vanadium complex (VC), supported by different analyses and validations. Moreover, it had a great performance when compared to the general AMBER force field. Beyond that, MD findings provided an in-depth perspective of vanadium complex-protein interactions that should be taken into consideration in future studies.
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Affiliation(s)
- Camila A Tavares
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Taináh M R Santos
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Elaine F F da Cunha
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil
| | - Teodorico C Ramalho
- Laboratory of Molecular Modelling, Department of Chemistry, Federal University of Lavras, Lavras37200-000, MG, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové500 03, Czech Republic
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9
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de Andrade TFCB, Dos Santos HF, Fonseca Guerra C, Paschoal DFS. Computational Prediction of Tc-99 NMR Chemical Shifts in Technetium Complexes with Radiopharmaceutical Applications. J Phys Chem A 2022; 126:5434-5448. [PMID: 35930743 DOI: 10.1021/acs.jpca.2c01617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Tc-99m nucleus is the most used nuclide in radiopharmaceuticals designed for imaging diagnosis. The metal can exist in nine distinct oxidation states and forms distinct coordination complexes with a variety of chelating agents and geometries. These complexes are usually characterized through Tc-99 NMR that is very sensitive to the Tc coordination sphere. Therefore, predicting Tc-99 NMR might be useful to assist experimentalists in structural characterization. In the present study, we propose three computational protocols for predicting Tc-99 NMR chemical shifts based on density functional theory calculations using relativistic and nonrelativistic Hamiltonians: the relativistic Model 1, the nonrelativistic Model 2, and the empirical nonrelativistic Model 3. In Models 2 and 3, the NMR-DKH basis set was used for all atoms, including the Tc, for which it was developed here. All models were applied for a set of 41 Tc-complexes with metal oxidation states 0, I, and V, for which the Tc-99 chemical shift was available experimentally. The mean absolute deviation and the mean relative deviation were 67 ppm and 4.8% (Model 1), 92 ppm and 6.2% (Model 2), and 65 ppm and 4.9% (Model 3), respectively. Last, the effect of the explicit solvent was evaluated for the [TcO2(en)2]+─Tc(V) complex. The calculated results for the Tc-99 NMR chemical shift at SO-ZORA-SSB-D/TZ2P-ZORA/COSMO//TPSS/def2-SVP/IEF-PCM(UFF) show that the inclusion of 14 water molecules (first solvation shell) together with the implicit solvation model leads to an absolute deviation of only 7 ppm (0.3%) from the experimental value, indicating that the solvent effects play a key role in predicting Tc-99 NMR.
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Affiliation(s)
- Taís F C B de Andrade
- 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, Macaé, 27.971-525 Rio de Janeiro, Brasil
| | - 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, Minas Gerais, Brasil
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - 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, Macaé, 27.971-525 Rio de Janeiro, Brasil
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10
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Zimmermann T, Šebesta F, Burda JV. A new grand-canonical potential for the thermodynamic description of the reactions in solutions with constant pH. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Zou Y, Hu Y, Ge S, Zheng Y, Li Y, Liu W, Guo W, Zhang Y, Xu Q, Lai Y. Effective Virtual Screening Strategy toward heme-containing proteins: Identification of novel IDO1 inhibitors. Eur J Med Chem 2019; 184:111750. [DOI: 10.1016/j.ejmech.2019.111750] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/22/2019] [Accepted: 09/28/2019] [Indexed: 01/11/2023]
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12
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Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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13
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Mesterházy E, Lebrun C, Crouzy S, Jancsó A, Delangle P. Short oligopeptides with three cysteine residues as models of sulphur-rich Cu(i)- and Hg(ii)-binding sites in proteins. Metallomics 2018; 10:1232-1244. [DOI: 10.1039/c8mt00113h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptides mimicking sulphur-rich fragments found in metallothioneins display unexpectedly different behaviours with the two metal ions Hg(ii) and Cu(i).
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Affiliation(s)
- Edit Mesterházy
- INAC/SYMMES/Université Grenoble Alpes
- CEA
- CNRS
- 38000 Grenoble
- France
| | - Colette Lebrun
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Serge Crouzy
- BIG/LCBM/Université Grenoble Alpes
- CEA
- CNRS
- (UMR 5249)
- 38000 Grenoble
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry
- University of Szeged
- Szeged H-6720
- Hungary
| | - Pascale Delangle
- INAC/SYMMES/Université Grenoble Alpes
- CEA
- CNRS
- 38000 Grenoble
- France
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14
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Discovery of imidazoleisoindole derivatives as potent IDO1 inhibitors: Design, synthesis, biological evaluation and computational studies. Eur J Med Chem 2017; 140:293-304. [DOI: 10.1016/j.ejmech.2017.09.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/20/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022]
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15
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Zhou J, Smith MD, Cooper CJ, Cheng X, Smith JC, Parks JM. Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10595-10604. [PMID: 28806072 DOI: 10.1021/acs.est.7b02204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellular uptake and export are important steps in the biotransformation of mercury (Hg) by microorganisms. However, the mechanisms of transport across biological membranes remain unclear. Membrane-bound transporters are known to be relevant, but passive permeation may also be involved. Inorganic HgII and methylmercury ([CH3HgII]+) are commonly complexed with thiolate ligands. Here, we have performed extensive molecular dynamics simulations of the passive permeation of HgII and [CH3HgII]+ complexes with thiolate ligands through a model bacterial cytoplasmic membrane. We find that the differences in free energy between the individual complexes in bulk water and at their most favorable position within the membrane are ∼2 kcal mol-1. We provide a detailed description of the molecular interactions that drive the membrane crossing process. Favorable interactions with carbonyl and tail groups of phospholipids stabilize Hg-containing solutes in the tail-head interface region of the membrane. The calculated permeability coefficients for the neutral compounds CH3S-HgII-SCH3 and CH3HgII-SCH3 are on the order of 10-5 cm s-1. We conclude that small, nonionized Hg-containing species can permeate readily through cytoplasmic membranes.
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Affiliation(s)
- Jing Zhou
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Micholas Dean Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Xiaolin Cheng
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jerry M Parks
- Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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16
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Discovery of potent IDO1 inhibitors derived from tryptophan using scaffold-hopping and structure-based design approaches. Eur J Med Chem 2017; 138:199-211. [DOI: 10.1016/j.ejmech.2017.06.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 06/07/2017] [Accepted: 06/22/2017] [Indexed: 11/18/2022]
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17
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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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18
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Zou Y, Wang F, Wang Y, Guo W, Zhang Y, Xu Q, Lai Y. Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations. Eur J Med Chem 2017; 131:152-170. [PMID: 28319781 DOI: 10.1016/j.ejmech.2017.03.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 10/20/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design.
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Affiliation(s)
- Yi Zou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China
| | - Fang Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Wenjie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, PR China.
| | - Yisheng Lai
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China.
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19
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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