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Oliveira AC, Filipe HAL, Geraldes CF, Voth GA, Moreno MJ, Loura LMS. Interaction of MRI Contrast Agent [Gd(DOTA)] - with Lipid Membranes: A Molecular Dynamics Study. Inorg Chem 2024; 63:10897-10914. [PMID: 38795015 PMCID: PMC11186012 DOI: 10.1021/acs.inorgchem.4c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/27/2024]
Abstract
Contrast agents are important imaging probes in clinical MRI, allowing the identification of anatomic changes that otherwise would not be possible. Intensive research on the development of new contrast agents is being made to image specific pathological markers or sense local biochemical changes. The most widely used MRI contrast agents are based on gadolinium(III) complexes. Due to their very high charge density, they have low permeability through tight biological barriers such as the blood-brain barrier, hampering their application in the diagnosis of neurological disorders. In this study, we explore the interaction between the widely used contrast agent [Gd(DOTA)]- (Dotarem) and POPC lipid bilayers by means of molecular dynamics simulations. This metal complex is a standard reference where several chemical modifications have been introduced to improve key properties such as bioavailability and targeting. The simulations unveil detailed insights into the agent's interaction with the lipid bilayer, offering perspectives beyond experimental methods. Various properties, including the impact on global and local bilayer properties, were analyzed. As expected, the results indicate a low partition coefficient (KP) and high permeation barrier for this reference compound. Nevertheless, favorable interactions are established with the membrane leading to moderately long residence times. While coordination of one inner-sphere water molecule is maintained for the membrane-associated chelate, the physical-chemical attributes of [Gd(DOTA)]- as a MRI contrast agent are affected. Namely, increases in the rotational correlation times and in the residence time of the inner-sphere water are observed, with the former expected to significantly increase the water proton relaxivity. This work establishes a reference framework for the use of simulations to guide the rational design of new contrast agents with improved relaxivity and bioavailability and for the development of liposome-based formulations for use as imaging probes or theranostic agents.
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Affiliation(s)
- Alexandre C. Oliveira
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- CPIRN-IPG—Center
of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - Carlos F.G.C. Geraldes
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-393 Coimbra, Portugal
- CIBIT/ICNAS
- Instituto de Ciências Nucleares Aplicadas à Saúde, Pólo das Ciências
da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, James Franck
Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Maria João Moreno
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CNC−Center
for Neuroscience and Cell Biology, University
of Coimbra, 3004-517 Coimbra, Portugal
| | - Luís M. S. Loura
- Coimbra
Chemistry Centre, Institute of Molecular
Sciences (CQC-IMS), 3004-535 Coimbra, Portugal
- Faculty
of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
- CNC−Center
for Neuroscience and Cell Biology, University
of Coimbra, 3004-517 Coimbra, Portugal
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Bellotti D, Leveraro S, Remelli M. Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods. Methods Enzymol 2023; 687:279-341. [PMID: 37666636 DOI: 10.1016/bs.mie.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.
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Affiliation(s)
- Denise Bellotti
- University of Ferrara, Department of Chemical, Pharmaceutical and Agricultural Sciences, via L. Borsari, Ferrara, Italy; Faculty of Chemistry, University of Wrocław, F. Joliot-Curie, Wrocław, Poland
| | - Silvia Leveraro
- University of Ferrara, Department of Chemical, Pharmaceutical and Agricultural Sciences, via L. Borsari, Ferrara, Italy
| | - Maurizio Remelli
- University of Ferrara, Department of Chemical, Pharmaceutical and Agricultural Sciences, via L. Borsari, Ferrara, Italy.
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Oliveira A, Filipe HAL, Ramalho JP, Salvador A, Geraldes CFGC, Moreno MJ, Loura LMS. Modeling Gd 3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents. Inorg Chem 2022; 61:11837-11858. [PMID: 35849762 PMCID: PMC9775472 DOI: 10.1021/acs.inorgchem.2c01597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The correct parametrization of lanthanide complexes is of the utmost importance for their characterization using computational tools such as molecular dynamics simulations. This allows the optimization of their properties for a wide range of applications, including medical imaging. Here we present a systematic study to establish the best strategies for the correct parametrization of lanthanide complexes using [Gd(DOTA)]- as a reference, which is used as a contrast agent in MRI. We chose the bonded model to parametrize the lanthanide complexes, which is especially important when considering the study of the complex as a whole (e.g., for the study of the dynamics of its interaction with proteins or membranes). We followed two strategies: a so-called heuristic approach employing strategies already published by other authors and another based on the more recent MCPB.py tool. Adjustment of the Lennard-Jones parameters of the metal was required. The final topologies obtained with both strategies were able to reproduce the experimental ion to oxygen distance, vibrational frequencies, and other structural properties. We report a new strategy to adjust the Lennard-Jones parameters of the metal ion in order to capture dynamic properties such as the residence time of the capping water (τm). For the first time, the correct assessment of the τm value for Gd-based complexes was possible by recording the dissociative events over up to 10 μs all-atom simulations. The MCPB.py tool allowed the accurate parametrization of [Gd(DOTA)]- in a simpler procedure, and in this case, the dynamics of the water molecules in the outer hydration sphere was also characterized. This sphere was divided into the first hydration layer, an intermediate region, and an outer hydration layer, with a residence time of 18, 10 and 19 ps, respectively, independent of the nonbonded parameters chosen for Gd3+. The Lennard-Jones parameters of Gd3+ obtained here for [Gd(DOTA)]- may be used with similarly structured gadolinium MRI contrast agents. This allows the use of molecular dynamics simulations to characterize and optimize the contrast agent properties. The characterization of their interaction with membranes and proteins will permit the design of new targeted contrast agents with improved pharmacokinetics.
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Affiliation(s)
- Alexandre
C. Oliveira
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hugo A. L. Filipe
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,CPIRN-IPG-Center
of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal
| | - João P.
Prates Ramalho
- Hercules
Laboratory, LAQV, REQUIMTE, Department of Chemistry, School of Science
and Technology, University of Évora, 7000-671 Évora, Portugal
| | - Armindo Salvador
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,CNC−Center
for Neuroscience and Cell Biology, University
of Coimbra, P-3004-517 Coimbra, Portugal,Institute
for Interdisciplinary Research - University of Coimbra, Casa Costa Alemão- Polo II, Rua D. Francisco de Lemos, 3030-789 Coimbra, Portugal
| | - Carlos F. G. C. Geraldes
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,Department
of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-393 Coimbra, Portugal,CIBIT/ICNAS
- Instituto de Ciências Nucleares Aplicadas à Saúde, Pólo das Ciências
da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
| | - Maria João Moreno
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal,
| | - Luís M. S. Loura
- Coimbra
Chemistry Center - Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal,Faculty
of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal,
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Utomo RY, Okada S, Sumiyoshi A, Aoki I, Nakamura H. Development of an MRI contrast agent for both detection and inhibition of the amyloid-β fibrillation process. RSC Adv 2022; 12:5027-5030. [PMID: 35425501 PMCID: PMC8981495 DOI: 10.1039/d2ra00614f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
A curcumin derivative conjugated with Gd-DO3A (Gd-DO3A-Comp.B) was synthesised as an MRI contrast agent for detecting the amyloid-β (Aβ) fibrillation process. Gd-DO3A-Comp.B inhibited Aβ aggregation significantly and detected the fibril growth at 20 μM of Aβ with 10 μM of probe concentration by T1-weighted MR imaging. A curcumin derivative conjugated with Gd-DO3A (Gd-DO3A-Comp.B) was developed to significantly inhibit the amyloid-β (Aβ) aggregation and detect the fibril growth by T1-weighted MR imaging.![]()
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Affiliation(s)
- Rohmad Yudi Utomo
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan
| | - Satoshi Okada
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan .,JST, PRESTO 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan
| | - Akira Sumiyoshi
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
| | - Ichio Aoki
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan
| | - Hiroyuki Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori Yokohama Kanagawa 226-8503 Japan
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