Conformational Changes of Drew–Dickerson Dodecamer in the Presence of Caffeine

Caffeine has always aroused great interest, many of its physiological effects have been known since ancient times, and nowadays it has become a substance of interest due to the evidence that has been found regarding its interaction with oncological drugs and the DNA chains. To elucidate the interaction of caffeine with DNA, a molecular mechanics study was performed with the Barcelona Supercomputing Center 1 force field with a fixed number of atoms, a fixed volume, and a fixed temperature also called NVT ensemble. A molecular docking was done using AutoDock 4.2, and then the configurations with the lowest interaction energy were subjected to a molecular dynamic simulation with the software AMBER19. It was found that the changes generated by the interaction of Caffeine in the minor grove of the Drew–Dickerson dodecamer in the ninth and tenth nucleotides (cytokine and guanine) in the torsion angles are an increase of 9.8° in angle α, a decrease of 18.7° in angle β, an increase of 12.2° in angle γ, a decrease of 26.5° in angle δ, an increase of 29.7° in angle ε, a slight decrease of 2.9° in the angle ζ, and a decrease of 30° in the angle χ.