Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA

We present an in silico study of the deintercalation of berubicin from two double-stranded oligonucleotide DNA sequences using well-tempered metadynamics (WT-MetaD), an enhanced sampling method widely employed for biomolecular systems. In our recent study (Mikaelian, G. J. Phys. Chem. B 2024, 128(26), 6291-6307), the thermodynamics of DNA-berubicin complexes in the intercalated state was examined in detail. Continuing this study here, we focus on the thermodynamics and kinetics of deintercalation, undertaking a rigorous analysis of individual stages in its mechanism. The Gibbs energy surface is first calculated as a function of two collective variables (used in prior studies of anthracyclines), followed by an estimation of deintercalation times. These deintercalation times are comparable to─or even exceed─those of clinically established anthracyclines in widespread therapeutic use. Our simulations reveal that the deintercalation mechanism involves two stable states─the intercalated state and the minor groove-bound state─as well as a reshuffling state. This three-step mechanism that emerges is supported by other published studies concerning DNA-anthracycline complexes. The rate-limiting step of the deintercalation mechanism is the transition from the intercalated to the reshuffling state, and the applied method allows a detailed description of it. Each state is described in terms of various properties, whose values are consistent with published computational and experimental studies on the interactions of other anthracyclines with DNA.