Molecular mechanism, binding free energy, and sequence selectivity of intercalation of doxorubicin and DNA

Abstract

Many drugs interact noncovalently with DNA either by groove binding or intercalation. Intercalation is a key process in drug discovery and biosensor development. Doxorubicin (DOX) is an intercalator drug that treats a wide range of cancers. However, its binding process with DNA is still a highly debatable topic on both the experimental and theoretical sides with many unanswered questions. Particularly, what is the key physical factor(s) that drives the complex formation at both conformational change and insertion binding stages? What are the DOX sequence-selectivity and the role of physical factors in determining this selectivity? What is the best model to describe the relationship between binding affinity and selectivity of an intercalator drug? How do the aqueous environment and ionic concentration impact the intercalation process? A comprehensive microsecond time-scale molecular dynamics study in an explicit aqueous solvent has been performed to address the above-raising questions. In this study, DOX interacts with different dsDNA sequences of various lengths (hexamer or tetradecamer). The molecular mechanics Poisson-Boltzmann or generalized-Born surface area (MM-PB(GB)SA) method is adapted to quantify and partition the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions and different DNA sequences. Our results show that the compulsory DNA conformational changes to form the intercalation cavity, the loss of translational and rotational mobility upon complex formation, and the overall electrostatic interactions are all unfavorable for the DOX-DNA complexation process. However, they are counteracted by the favorable contributions from the attractive van der Waals interaction, the non-polar solvation interaction, the vibrational entropic contribution, and the polyelectrolyte free energy at lower ionic strength. The van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)2 or (TA)2 driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings indicate that the aqueous bathing solution (i.e. water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that this process preferably occurs at low ionic strength and is crucially dependent on solvent effects.