Combined MD/QTAIM techniques to evaluate ligand-receptor interactions. Scope and limitations

In medicinal chemistry, it is extremely important to evaluate, as accurately as possible, the molecular interactions involved in the formation of different ligand-receptor (L-R) complexes. Evaluating the different molecular interactions by quantum mechanics calculations is not a simple task, since formation of an L-R complex is a dynamic process. In this case, the use of combined techniques of molecular dynamics (MD) and quantum calculations is one the best possible approaches. In this work we report a comparative study using combined MD and QTAIM (Quantum Theory of Atoms In Molecules) calculations for five biological systems with different levels of structural complexity. We have studied Acetylcholinesterase (AChE), D2 Dopamine Receptor (D2DR), beta Secretase (BACE1), Dihydrofolate Reductase (DHFR) and Sphingosine Kinase 1 (SphK1). In these molecular targets, we have analyzed different ligands with diverse structural characteristics. The inhibitory activities of most of them have been previously measured in our laboratory. Our results indicate that QTAIM calculations can be extremely useful for in silico studies. It is possible to obtain very accurate information about the strength of the molecular interactions that stabilize the formation of the different L-R complexes. Better correlations can be obtained between theoretical and experimental data by using QTAIM calculations, allowing us to discriminate among ligands with similar affinities. QTAIM analysis gives fairly accurate information for weak interactions which are not well described by MD simulations. QTAIM study also allowed us to evaluate and determine which parts of the ligand need to be modified in order to increase its interactions with the molecular target. In this study we have discussed the importance of combined MD/QTAIM calculations for this type of simulations, showing their scopes and limitations.

Self-Assembly of Aluminum- and Gallium-Based meso-Metallaporphyrins

The molecular meso-metallaporphyrin has been obtained from the reaction of AlMe₃ with the bulky 4,5-(Ph₂(HO)C)₂-1,2,3-triazole (1). The presence of Al-Me groups coordinated to the triazole rings creates three different stereoisomers that were identified by single-crystal X-ray diffraction. Further studies revealed that, for steric reasons, only one of the two main stereoisomers is active in the polymerization of ε-caprolactone. When GaMe₃ is used instead of AlMe₃, a trimetallic species is formed instead of the meso-metallaporphyrin pointing to a metal-directed self-assembly. On the other hand, the reaction of the monolithium salt [{Li(THF)₂}{κ²- N, N'-4,5-(Ph₂(HO)C)-1,2,3-triazole}]₂ (2; THF = tetrahydrofuran) with MCl₃ (M = Al, Ga) yields meso-metallaporphyrin species with a lithium atom in the center of the metallacycle. While the gallium derivative is rather stable in solution, the aluminum analogue decomposes rapidly. In the solid state, continuous cationic columns running throughout the whole crystal are formed from alternating Li⊂[M]₄ (M = Al, Ga) meso-metallaporphyrin and [Li(THF)₄]⁺ cations. Density functional theory calculations determined that the weak Cl···H, H···H, N···H, and Cl···O interactions with a total interaction energy of -38.6 kcal·mol^-1 are responsible for this unusual packing.

The Role of the DNA Backbone in Minor-Groove Ligand Binding

Molecular recognition between ligands and nucleic acids plays a key role in therapeutic activity. Some molecules interact with DNA in a nonbonded manner through intercalation or through the DNA grooves. The recognition of minor-groove binders is attributed to a set of hydrogen-bonding interactions between the binders and the hydrogen-bond-acceptor groups on the groove floor and walls. It is commonly considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity. However, our group has found that the deoxyribose rings have a central function in the recognition and the intercalation of metal complexes into DNA. Herein, we determined the specific interactions between the binder CGP 40215A and the minor-groove atoms, based on the local properties of electron density. We found that specific interactions between the deoxyribose moiety within the backbone of DNA and the binder are essential for molecular recognition, and they are responsible for one third of the interaction energy.