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.

Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone

The influence of hydrogen bonds in model intercalated systems between guanine-cytosine and adenine-thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10-phenanthroline (phen) and derivatives obtained by substitution with OH and NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6-DH2, M06-2X and B3LYP-D3 along with the recently developed near linear-scaling coupled cluster method DLPNO-CCSD(T) for benchmark calculations. Our results given by QTAIM and non-covalent interaction analysis confirmed the existence of hydrogen bonds created by OH and NH2 . The trends in the energy decomposition analysis for the interaction energy, ΔEint , showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp . Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by OH and NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint . The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.

Greener Strategy for Lupanine Purification from Lupin Bean Wastewaters Using a Molecularly Imprinted Polymer

Lupanine is an alkaloid used in the pharma industry as a building block or precursor in the synthesis of sparteine and also explored for drug synthesis in the pharma industry as a chiral selector. This alkaloid is found in lupin bean processing wastewaters originated from the debittering process to make these beans edible. In this work, a computational chemistry approach was taken to design molecularly imprinted polymers (MIPs) selecting itaconic acid, a biobased building block, as a functional monomer that can provide higher affinities for lupanine. MIP-1 was prepared using lupanine as the template, itaconic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linker by bulk polymerization. Lupanine was concentrated from lupin bean wastewater by nanofiltration, extracted with ethyl acetate, and purified using the synthesized MIP. MIP-1 was able to selectively recognize lupanine and improve the purity of lupanine from 78 to 88%, with 82% recovery of the alkaloid. These results show the potential application of this strategy to render the industrial process more sustainable.

Semi-empirical and Linear-Scaling DFT Methods to Characterize duplex DNA and G-quadruplexes in 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...

From groove binding to intercalation: unravelling the weak interactions and other factors modulating the modes of interaction between methylated phenanthroline-based drugs and duplex DNA

Several antitumor drugs base their cytotoxicity on their capacity to intercalate between base pairs of DNA. Nevertheless, it has been established that the mechanism of intercalation of drugs in DNA starts with the prior groove binding mode of interaction of the drug with DNA. Sometimes, for some kind of flat small molecules, groove binding does not produce any cytotoxic effect and the fast transition of such flat small molecules to the cytotoxic intercalation mode is desirable. This is the case of methylated phenanthroline (phen) derivatives, where, changes in the substitution in the position and number of methyl groups determine their capability as cytotoxic compounds and, therefore, it is a way for the modulation of cytotoxic effects. In this work, we studied this modulation by means of the interaction of the [Pt(en)(phen)]²⁺ complex and several derivatives by methylation of phen in different number and position and the d(GTCGAC)₂ DNA hexamer via groove binding using PM6-DH2 and DFT-D methods. The analysis of the geometries, electronic structure and energetics of the studied systems was compared to experimental works to gain insight into the relation structure-interaction for the studied systems with cytotoxicity. The trends are explained by means of the Non-Covalent Interaction (NCI) index, the Energy Decomposition Analysis (EDA) and solvation contributions. Our results are in agreement with the experiments, in which the methylation of position 4 of phen seems to favour the interaction via groove binding thus making the transition to the intercalation cytotoxic mode difficult. Looking at the NCI results, these interactions come not only from the CH/π and CH/n interactions of the methyl group in position 4 but also from the ethylenediamine (en) ligand, whose orientation in the Pt complex was found in such a way that it produces a high number of weak interactions with DNA, especially with the sugar and phosphate backbone.

Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes

G-quadruplexes have drawn widespread attention for serving as a potential anti-cancer target and their application in material science. Molecular dynamics (MD) simulation is the key theoretical tool in the study of GQ's structure-function relationship. In this article, we systematically benchmarked the five force fields of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 on the MD simulation of G-quadruplex from four aspects: structural stability, central ion channel stability, description of Hoogsteen hydrogen bond network, and description of the main chain dihedral angle. The results show that the overall performance of the Drude force field is the best. Although there may be a certain over-polarization effect, it is still the best choice for the MD simulation of G-quadruplexes.

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.

Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions

Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.

Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol³ code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.

Stacking interactions of the methylated cyclopentadienyl ligands in the crystal structures of transition metal complexes

In the crystal structures of methylated cyclopentadienyl (Cp) complexes (MeCp, Me₄Cp and Me₅Cp) deposited in the Cambridge Structural Database, certain orientation types of stacked contacts can be noted as the most frequent. These orientation preferences can be well explained by the matching of oppositely charged regions of electrostatic potential. Parallel displaced stacking, large offset stacking and C-H...π interactions are the dominant interaction types that are responsible for the arrangement in the crystal structures of stacked methylated Cp complexes.

Molybdenum(ii) complexes with p-substituted BIAN ligands: synthesis, characterization, biological activity and computational study

New complexes [Mo(η3-C3H5)X(CO)2(4-Y-BIAN)] (4-Y-BIAN = bis(4-Y-phenyl)-acenaphthenequinonediimine), with X = Br and Y = H, Me, OMe, COOH and X = Cl, Y = OMe, as well as the cation with X = NCMe and Y = OMe were synthesized, expanding the scope of this family. Two single crystal X-ray structures (X = Br, Y = Me, OMe) display a less symmetric arrangement (axial isomer), where one N donor atom is trans to the allyl group and the second to one CO. DFT studies showed similar energies for the two possible isomers of the complexes, with a very small preference for the observed axial isomer. The HOMO of the complexes is localized in the metal and the HOMO-1 of the oxidized species has a contribution from the BIAN ligand, while the LUMO is fully localized in BIAN. Electrochemical studies showed one process corresponding to the oxidation of Mo(ii) to Mo(iii) for complexes with X = Br, Y = H, Me, and two oxidation reactions for those with X = Br, Y = Cl, OMe, while the COOH derivative exhibited no oxidation wave. The antitumor effect of the complexes with X = Br was tested in cancer lines, and the H and OMe complexes were particularly active, with EC50 values below 8 μM in HeLa cell lines. The DNA binding constants determined by titration experiments were comparable with those of doxorubicin and ethidium bromide, suggesting a mechanism of action based on intercalation in DNA.

Two Highly Stable Luminescent Lead Phosphonates Based on Mixed Ligands: Highly Selective and Sensitive Sensing for Thymine Molecule and VO3 - Anion

Two luminescent lead phosphonates with two-dimensional (2D) layer and three-dimensional (3D) framework structure, namely, Pb₃[(L₁)₂(Hssc)(H₂O)₂] (1) and [Pb₂(L₂)_0.5(bts)(H₂O)₂]·H₂O (2) (H₂L₁ = O(CH₂CH₂)₂NCH₂PO₃H₂, H₄L₂ = H₂PO₃CH₂NH(C₂H₄)₂NHCH₂PO₃H₂, H₃ssc = 5-sulfosalicylic acid, NaH₂bts = 5-sulfoisophthalic acid sodium) have been prepared via hydrothermal techniques. The two compounds not only show excellent thermal stability but also remain intact in aqueous solution within an extensive pH range. Moreover, the atomic absorption spectroscopy analysis experiment indicates that there does not exist the leaching of Pb²⁺ ions from the lead phosphonates, which show they are nontoxic in aqueous solution. In compound 1, the Pb(1)O₄, Pb(2)O₇, Pb(3)O₄, and CPO₃ polyhedra are interlinked into a one-dimensional chain, which is further connected to adjacent chain by sharing the Hssc^2- to form a 2D layer. Interestingly, compound 1 as a highly selective and sensitive luminescent material can be used to detect the thymine molecule with a very low detection limit of 8.26 × 10^-7 M. In compound 2, the Pb(1)O₆ and Pb(2)O₅ polyhedra are interlinked into a dimer via edge sharing, which is further connected to adjacent dimer to form a tetramer via corner sharing, and such a tetramer is then interlinked into a 2D layer through bts^3- ligands; the adjacent 2D layers are finally constructed to a 3D structure by sharing the L₂ ^4- ligand. Compound 2 can be applied as an excellent luminescent sensor for sensing of VO₃ ^- anion. Furthermore, the probable fluorescent quenching mechanisms of the two compounds have also been studied.

Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study

The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.

Quantitative investigation of C–H⋯π and other intermolecular interactions in a series of crystalline N-(substituted phenyl)-2-naphthamide derivatives

In this study, we have investigated the nature and characteristics of different intermolecular interactions present in a series of sevenN-(substituted phenyl)-2-naphthamides.

Theoretical investigations on the phase transition of pure and Li-doped AlH3

The calculated Gibbs free energy change and enthalpy change for the γ → α phase transition and heat capacity indicate that the aluminum hydride synthesized in experiments is Li-doped.