In Silico Study of the Effect of Porphyrin-Based Ligands on the Structure of G-Quadruplex in the Presence of Different Ions

The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ4-pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ4-pyridine-4-yl) porphyrin (L3), with G-quadruplex in the presence of Li+, Na+ , K+ , Rb+ ,Cs+ ,Ca2+ ,Mg2+ ions was studied by density functional theory and molecular dynamics simulation. Single point energy calculations were performed on sampled structures from molecular dynamics simulations. Sampling was performed by free energy landscape (FEL) method. Quantum calculations were performed by B3LYP density functional method and 6-31G basis function. Quantum descriptors frontier orbital energies, ionization energy, chemical species hardness, chemical potential and the number of transferred electrons were calculated. The results show that loops and sheets of G-quadruplex are involved in interaction with ligands. The stability of the complex between ligands and G-quadruplex in the presence of K+ and Na+ ions is greater than the stability of the complex in the presence of Cs+ and Mg2+ ions.