Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands.

We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.5 kcal mol-1 above. On the other hand, the energy decomposition analysis (EDA) favours interaction energies for the systems containing the Eq isomer. However, when solvent effects are taken into account the systems containing the Ax isomer are again the most stable. This Ax isomer was found interacting by means of end-stacking with the GQ and surprisingly totally inside the non-canonical secondary structure, where all the ligands of the metal complex produce several weak interactions with the DNA structure. On the other hand, the Eq isomer prefers to interact from outside by means of intercalation in which the ancillary ligands also have some role in the interaction. Such features and comparison with the results regarding the interaction of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with duplex DNA suggest that the [Mo(η3-C3H5)Br(CO)2(phen)] would have a higher affinity and eventual selectivity for non-canonical DNA GQ structures.

Semi-empirical and linear-scaling DFT methods to characterize duplex DNA and G-quadruplexes in the presence of interacting small molecules.

The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of such large and complex systems requires considering interactions of different types simultaneously in a balanced way, such as non-covalent weak interactions (namely hydrogen bonds and stacking), metal-ligand interactions, polarisation and charge transfer effects. All these considerations imply a real challenge for computational chemistry. The possibility of studying large biological systems using quantum methods for the entire system requires significant computational resources, with improvements in parallelisation and optimisation of theoretical strategies. Computational methods, such as Linear-Scaling Density Functional Theory (LS-DFT) and DLPNO-CCSD(T), may allow performing ab initio quantum mechanics calculations, including the electronic structure for large biological systems, in a reasonable computing time. In this work, we study the interaction of small molecules and cations with DNA (both duplex DNA and G-quadruplexes), comparing different computational methods: a LS-DFT method at the LMKLL/DZDP level of theory, semi-empirical methods (PM6-DH2 and PM7), mixed QM/MM, and DLPNO-CCSD(T). Our goal is to demonstrate the adequacy of LS-DFT to treat the different types of interactions present in DNA-dependent systems. We show that LMKLL/DZDP using SIESTA can yield very accurate geometries and energetics in all the different systems considered in this work: duplex DNA (dDNA), phenanthroline intercalating dDNA, G-quadruplexes, and metal-G-tetrads considering alkaline metals of different sizes. As far as we know, this is the first time that full G-quadruplex geometry optimisations have been carried out using a DFT method thanks to its linear-scaling capabilities. Moreover, we show that LS-DFT provides high-quality structures, and some semi-empirical Hamiltonians can also yield suitable geometries. However, DLPNO-CCSD(T) and LS-DFT are the only methods that accurately describe interaction energies for all the systems considered in our study.

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes.

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.

Computational Studies on the Binding Preferences of Molybdenum(II) Phenanthroline Complexes with Duplex DNA. The Important Role of the Ancillary Ligands.

The interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η3-C3H5)Br(CO)2(phen)] metal complex with DNA was studied by using large-scaling density functional theory methods including dispersion for the whole system, represented as a d(AGACGTCT)2 DNA octamer, to gain insight into its experimentally found cytotoxicity. Three different modes of interaction were considered: (1) minor groove (mg) binding, (2) intercalation through the major groove (MG), and (3) the apparently unexpected intercalation via the mg. Computed formation energies, energy decomposition analysis, solvation energies, and noncovalent interaction analysis explain the preference for Eq and Ax isomers of the complex for intercalation via the mg. π-π interactions of the phenanthroline (phen) flat ligand that appear in the intercalation mode and do not exist for the mg binding mode suggest the preference of [Mo(η3-C3H5)Br(CO)2(phen)] for intercalation. On the other hand, the role of the ancillary ligands is crucial for better interaction of the metal complex including phen than when the phen ligand alone is considered because of their additional interactions with base pairs (bps). The role of the ancillary ligands is enhanced when intercalation takes place through the mg because such ligands are able to interact not only with bps but also with the sugar and phosphate backbone, whereas for intercalation through the MG, the interaction of these ligands is only with bps. This feature explains the preference of [Mo(η3-C3H5)Br(CO)2(phen)] for intercalation via the mg in crystal structures. Finally, the solvation penalty is more important for intercalation through the mg than via the MG, which suggests a subtle mechanism involving weak interactions with solvent molecules to explain the selectivity for intercalation in solution to answer the MG versus mg question.

Learning to Model G-Quadruplexes: Current Methods and Perspectives.

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.

Role of Dispersion Interactions in Endohedral TM@(ZnS)12 Structures.

II-VI semiconducting materials are gaining attention due to their optoelectronic properties. Moreover, the addition of transition metals, TMs, might give them magnetic properties. The location and distance of the TM are crucial in determining such magnetic properties. In this work, we focus on small hollow (ZnS)12 nanoclusters doped with TMs. Because (ZnS)12 is a cage-like spheroid, the cavity inside the structure allows for the design of endohedral compounds resembling those of C60. Previous studies theoretically predicted that the first-row TM(ZnS)12 endohedral compounds were thermodynamically unstable compared to the surface compounds, where the TM atom is located at the surface of the cluster. The transition states connecting both structure families were calculated, and the estimated lifetimes of these compounds were predicted to be markedly small. However, in such works dispersion effects were not taken into account. Here, in order to check for the influence of dispersion on the possible stabilization of the desired TM(ZnS)12 endohedrally doped clusters, several functionals are tested and compare to MP2. It is found that the dispersion effects play a very important role in determining the location of the metals, especially in those TMs with the 4s3d shell half-filled or completely filled. In addition, a complete family of TM doped (ZnS)12 nanoclusters is explored using ab initio molecular dynamics simulations and local minima optimizations that could guide the experimental synthesis of such compounds. From the magnetic point of view, the Cr(7S)@(ZnS)12 compound is the most interesting case, since the endohedral isomer is predicted to be the global minimum. Moreover, molecular dynamics simulations show that when the Cr atom is located at the surface of the cluster, it spontaneously migrates toward the center of the cavity at room temperature.