The dynamics of water exchange in gadolinium DOTA complexes studied by transition path sampling and potential of mean force methods

Molecular Dynamics Studies of the Ho(III) Aqua-tris(dibenzoylmethane) Complex: Role of Water Dynamics

The seven-coordinate Ho(III) aqua-tris(dibenzoylmethane)(DBM) complex, referred to as Ho-(DBM)₃·H₂O, was first reported in the late 1960s. It has a threefold symmetric structure, with Ho at the center of three dibenzoylmethane ligands and hydrogen-bonded water to ligands. It is considered that the hydrogen bonds between the water molecule and the ligands surrounding Ho play an important role in the formation of its symmetrical structure. In this work, we developed new force-field parameters for classical molecular dynamics (CMD) simulations to theoretically elucidate the structure and dynamics of Ho-(DBM)₃·H₂O. To develop the force field, structural optimization and molecular dynamics were performed on the basis of ab initio calculations using the plane-wave pseudopotential method. The force-field parameters for CMD were then optimized to reproduce the data obtained from ab initio calculations. Validation of the developed force field showed good agreement with the experimental crystalline structure and ab initio data. The vibrational properties of water in Ho-(DBM)₃·H₂O were investigated by comparison with bulk liquid water. The vibrational motion of water was found to have a characteristic mode originating from stationary rotational motion along the c-axis of Ho(III) aqua-tris(dibenzoylmethane). Contrary to expectations, the hydrogen-bond dynamics of water in Ho-(DBM)₃·H₂O were found to be almost equivalent to those of bulk liquid water except for librational motion. This development route for force-field parameters for CMD and the establishment of water dynamics can advance the understanding of water-coordinated metal complexes with high coordination numbers such as Ho-(DBM)₃·H₂O.

Modeling Gd3+ Complexes for Molecular Dynamics Simulations: Toward a Rational Optimization of MRI Contrast Agents

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 (τ_m). For the first time, the correct assessment of the τ_m 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.

Crystal Structures of DOTMA Chelates from Ce3+ to Yb3+ : Evidence for a Continuum of Metal Ion Hydration States

The crystal structures of chelates formed between each stable paramagnetic lanthanide ion and the octadentate polyamino carboxylate ligand DOTMA are described. A total of 23 individual chelates structures were obtained; in each chelate the coordination geometry around the metal ion is best described as a twisted square antiprism (torsion angle -25.0°--31.4°). Despite the uniformity of the general coordination geometry provided by the DOTMA ligand, there is a considerable variation in the hydration state of each chelate. The early Ln³⁺ chelates are associated with a single inner sphere water molecule; the Ln-OH₂ interaction is remarkable for being very long. After a clear break at gadolinium, the number of chelates in the unit cell that have a water molecule interacting with the Ln³⁺ decreases linearly until at Tm³⁺ no water is found to interact with the metal ion. The Ln-OH₂ distance observed in the chelates of the later Ln³⁺ ions are also extremely long and increase as the ions contract (2.550-2.732 Å). No clear break between hydrated and dehydrated chelates is observed; rather this series of chelates appear to represent a continuum of hydration states in which the ligand gradually closes around the metal ion as its ionic radius decreases (with decreased hydration) and the metal drops down into the coordination cage.

Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C60-Lysozyme Model

Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.

Structure and properties of DOTA-chelated radiopharmaceuticals within the 225Ac decay pathway

The successful delivery of toxic cargo directly to tumor cells is of primary importance in targeted (α) particle therapy. Complexes of radioactive atoms with the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelating agent are considered as effective materials for such delivery processes. The DOTA chelator displays high affinity to radioactive metal isotopes and retains this capability after conjugation to tumor targeting moieties. Although the α-decay chains are well defined for many isotopes, the stability of chelations during the decay process and the impact of released energy on their structures remain unknown. The radioactive isotope 225Ac is an α-particle emitter that can be easily chelated by DOTA. However, 225Ac has a complex decay chain with four α-particle emissions during decay of each radionuclide. To advance our fundamental understanding of the consequences of α-decay on the stability of tumor-targeted 225Ac-DOTA conjugate radiopharmaceuticals, we performed first principles calculations of the structure, stability, and electronic properties of the DOTA chelator to the 225Ac radioactive isotope, and the initial daughters in the decay chain, 225Ac, 221Fr, 217At and 213Bi. Our calculations show that the atomic positions, binding energies, and electron localization functions are affected by the interplay between spin-orbit coupling, weak dispersive interactions, and environmental factors. Future empirical measurements may be guided and interpreted in light of these results.

Fullerenes and their derivatives as inhibitors of tumor necrosis factor-α with highly promoted affinities

Tumor necrosis factor-α (TNF-α) is a cell signalling protein involved in systemic inflammation in infectious and other malignant diseases. Physiologically, it plays an important role in regulating host defence, but its overexpression can lead to serious illnesses including cancer, autoimmune disease and inflammatory disease. Gadolinium-based metallofullerenols, e.g., Gd@C82(OH) x (x ≈ 22), are well known for their abundant biological activities with low toxicity experimentally and theoretically; however, their activity in direct TNF-α inhibition has not been explored. In this work, we investigated the inhibiting effects of four types of fullerene-based ligands: fullerenes, fullerenols, metallofullerenes, and metallofullerenols. We reported previously that fullerenes, metallofullerenes and their hydroxylated derivatives (fullerenols) can reside in the same pocket of the TNF-α dimer as that of SPD304-a known inhibitor of TNF-α [He et al. (2005) Science 310:1022, 18]. Ligand docking and binding free energy calculations suggest that, with a similar nonpolar interaction dominated binding pattern, the fullerene-based ligands, C60, C60(OH)12, Gd@C60, C82, C82(OH)12, Gd@C82, Gd@C82(OH)13 and Gd@C82(OH)21, have larger affinity than currently known inhibitors, and could be used to design novel inhibitors of TNF-α in the future. Graphical Abstract Fullerene-material/TNF-α.

Gadolinium MRI contrast agents based on triazine dendrimers: relaxivity and in vivo pharmacokinetics

Four gadolinium (Gd)-based macromolecular contrast agents, G3-(Gd-DOTA)(24), G5-(Gd-DOTA)(96), G3-(Gd-DTPA)(24), and G5-(Gd-DTPA)(96), were prepared that varied in the size of dendrimer (generation three and five), the type of chelate group (DTPA or DOTA), and the theoretical number of metalated chelates (24 and 96). Synthesis relied on a dichlorotriazine derivatized with a DOTA or DTPA ligand that was incorporated into the dendrimer and ultimately metalated with Gd ions. Paramagnetic characteristics and in vivo pharmacokinetics of all four contrast agents were investigated. The DOTA-containing agents, G3-(Gd-DOTA)(24) and G5-(Gd-DOTA)(96), demonstrated exceptionally high r1 relaxivity values at off-peak magnetic fields. Additionally, G5-(Gd-DOTA)(96) showed increased r1 relaxivity in serum compared to that in PBS, which was consistent with in vivo images. While G3-(Gd-DOTA)(24) and G3-(Gd-DTPA)(24) were rapidly excreted into the urine, G5-(Gd-DOTA)(96) and G5-(Gd-DTPA)(96) did not clear as quickly through the kidneys. Molecular simulation of the DOTA-containing dendrimers suggests that a majority of the metalated ligands are accessible to water. These triazine dendrimer-based MRI contrast agents exhibit several promising features such as high in vivo r1 relaxivity, desirable pharmacokinetics, and well-defined structure.

Water exchange of a ProHance MRI contrast agent: isomer-dependent free-energy landscapes and mechanisms

The water-exchange reaction in two diastereoisomers of the clinical magnetic resonance imaging contrast agent [Gd(HP-DO3A)(H(2)O)] (also known as ProHance) has been studied using ab initio simulations. On the basis of the molecular-level details of the mechanism derived from these simulations in aqueous solution, we unravel the underlying difference in the free energies and mechanisms of water exchange in the two diastereoisomers. These findings reveal the crucial role played by hydrogen-bonding dynamics and thus suggest their appropriate control in tailoring improved gadolinium-based constrast agents.

Conformational behaviour determines the low-relaxivity state of a conditional MRI contrast agent

The conformational behaviour in aqueous solution of the EgadMe complex, a conditional gadolinium-based contrast agent sensitive to beta-galactosidase enzymatic activity, is investigated by means of ab initio calculations and classical molecular dynamics simulations. Furthermore, force field parameterization of gadolinium-ligand interactions is performed, and its reliability is tested on the bench mark [Gd(DOTA)](-) system by MD simulations. Both computational methods highlight the presence in EgadMe of two main conformational isomers. The lowest energy conformation is a "close" form, corresponding to a state of low-relaxivity (MRI "inactive"), in which the ninth coordination site of the gadolinium ion is occupied by one oxygen atom of the galactopyranose residue. The second isomer, which is 2.9 (at ab initio level) and 4.2 (at MD level) kcal mol(-1) above the global minimum, presents an "open" form, corresponding to a state of high-relaxivity (MRI "active") in which one water molecule coordinates the ion. These results are consistent with experimental findings reported for EgadMe, and show that competition at the ninth coordination site of gadolinium ion, between the intra (the galactopyranose residue) and inter (water molecules) molecular interactions, affects the relaxivity of this system.

Gadolinium(III) complexes as MRI contrast agents: ligand design and properties of the complexes

Magnetic resonance imaging is a commonly used diagnostic method in medicinal practice as well as in biological and preclinical research. Contrast agents (CAs), which are often applied are mostly based on Gd(III) complexes. In this paper, the ligand types and structures of their complexes on one side and a set of the physico-chemical parameters governing properties of the CAs on the other side are discussed. The solid-state structures of lanthanide(III) complexes of open-chain and macrocyclic ligands and their structural features are compared. Examples of tuning of ligand structures to alter the relaxometric properties of gadolinium(III) complexes as a number of coordinated water molecules, their residence time (exchange rate) or reorientation time of the complexes are given. Influence of the structural changes of the ligands on thermodynamic stability and kinetic inertness/lability of their lanthanide(III) complexes is discussed.

Ab initio simulation of a gadolinium-based magnetic resonance imaging contrast agent in aqueous solution

The first ab initio molecular dynamics simulation of a Gd(III)-based contrast agent in explicit aqueous solution at ambient conditions as used in the actual magnetic resonance imaging of human bodies is presented. The description of the structure of this chelate complex is considerably improved with respect to typical force fields and ab initio calculations in continuum solvent models if the open 4f shell of Gd is included explicitly. The solvation-shell structure is revealed to be anionic and includes a rather short hydrogen bond donated by the hydroxypropyl arm.