Amodiaquine Nonspecifically Binds Double Stranded and Three‐Way Junction DNA Structures

The 4‐aminoquinoline class of compounds includes the important antimalarial compounds amodiaquine and chloroquine. Despite their medicinal importance, the mode of action of these compounds is poorly understood. In a previous study we observed these compounds, as well as quinine and mefloquine, tightly bind the DNA cocaine‐binding aptamer. Here, we further explore the range of nucleic acid structures bound by these compounds. To gauge a wide range of binding affinities, we used isothermal titration calorimetry to explore high affinity binding (nM to tens of μM) and NMR spectroscopy to assay weak binding biding in the hundreds of micromolar range. We find that amodiaquine tightly binds all double stranded DNA structures explored. Mefloquine binds double stranded DNA duplex molecules tightly and weakly associates with a three‐way junction DNA construct. Quinine and chloroquine only weakly bind duplex DNA but do not tightly bind any of the DNA constructs explored. A simulation of the free energy of binding of these ligands to the Dickerson‐Drew dodecamer resulted in an excellent agreement between the simulated and experimental free energy. These results provide new insight into the DNA binding of clinically important antimalarial compounds and may play a role in future development of new antimalarials. The binding of amodiaquine, mefloquine, chloroquine and quinine to different DNA structures was studied using isothermal titration calorimetry and nuclear magnetic resonance spectroscopy. Amodiaquine tightly binds to all DNA structures studied while other ligands are more selective in which DNA structures they bind. Trends in calculated binding free energy versus the experimental results of amodiaquine binding a DNA dodecamer match.