Doxorubicin (DOX) is an anthracycline anticancer agent whose activity is closely linked to DNA binding. The structural mechanisms by which metal coordination affects DOX–DNA association are not well defined. This study combined computational chemistry and spectroscopic experiments to investigate how Cu(II) coordination alters DOX structure and its recognition of DNA.
The authors used density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations to probe conformational and electronic changes in DOX upon complexation with Cu(II) and to model DOX interactions with DNA. Complementary UV–Vis and competitive fluorescence experiments were performed to test whether the computationally predicted changes correspond to measurable alterations in DNA binding.
DFT was applied to characterize the structural and electronic properties of the free DOX molecule and the Cu(II)-DOX complex. Molecular docking provided initial poses for DOX association with DNA, and MD simulations assessed the stability and dynamics of the predicted DOX–DNA complexes over time. These computational approaches were integrated to evaluate both intrinsic changes in DOX induced by metal coordination and the resulting capacity of the ligand to adopt DNA-compatible binding modes.
DFT-based characterization of the Cu(II)-DOX complex identified coordination-induced changes in both structure and electronic distribution. The calculations indicated a reduction in conformational freedom and an increase in molecular rigidity upon coordination to Cu(II). These DFT-derived observations were interpreted as favoring DOX conformations that are more compatible with intercalative binding to nucleic acids.
The study abstract reports these DFT findings as consistent with a hypothesis that metal coordination biases DOX toward an intercalation-compatible configuration. Specific DFT parameters, functionals, basis sets, and quantitative electronic descriptors were not reported in the abstract.
Molecular docking and subsequent MD simulations supported a stable intercalative association of DOX with DNA in the computational models applied. Docking provided plausible intercalation poses, and MD simulations showed persistence of those poses over the simulation timeframes used, indicating that the modeled complexes were dynamically stable.
These computational results are presented in the source as complementary to the DFT-derived notion of reduced conformational flexibility: a more rigid DOX species resulting from Cu(II) coordination is postulated to more readily adopt and sustain intercalative interactions with DNA.
UV–Vis spectroscopy experiments were used to probe DOX–DNA interactions in solution and to assess the effect of Cu(II) coordination on apparent binding. The abstract reports that UV–Vis analysis indicated a substantial, approximately tenfold increase in apparent DNA-binding affinity when DOX was coordinated to Cu(II) compared with the uncoordinated drug.
The magnitude of this increase is reported as an experimental observation supporting the computational hypothesis that coordination stabilizes an intercalation-compatible DOX configuration. Detailed experimental conditions, such as concentrations, buffers, titration methods, and binding models used to derive apparent affinities, are not provided in the abstract.
Competitive fluorescence assays employing ethidium bromide were conducted to evaluate how Cu(II) coordination influences DOX competition for DNA binding sites. The fluorescence measurements showed pronounced perturbation of DNA-associated ethidium bromide signal in the presence of Cu(II)-DOX, consistent with altered DNA binding behavior relative to uncoordinated DOX.
These fluorescence data are presented as corroborative evidence that coordination to Cu(II) modifies DOX recognition of DNA and affects competitive displacement of intercalating probes. The abstract does not provide quantitative fluorescence values or the detailed experimental protocol.
Taken together, the computational and spectroscopic results create a coherent picture: Cu(II) coordination produces structural and electronic changes in DOX that reduce conformational freedom and increase rigidity, and these changes favor conformations compatible with intercalation into DNA. Computational docking and MD simulations indicate stable intercalative complexes, while UV–Vis and fluorescence experiments substantiate a substantial increase in apparent DNA-binding affinity and altered competitive binding behavior.
The study interprets these aligned findings to establish a mechanistic link between metal coordination, DOX conformational modulation, and DNA recognition.
The authors highlight metal coordination as a potential strategy to tune the biomolecular interactions of anthracycline therapeutics such as doxorubicin. By modulating ligand conformation and DNA affinity through metal complexation, it may be possible to influence pharmacodynamic properties relevant to anticancer activity.
Limitations and details not reported in the abstract include full experimental conditions, quantitative DFT parameters, explicit docking scores, MD simulation lengths and conditions, and complete spectroscopic datasets. These specifics would be necessary to fully evaluate reproducibility and to translate the findings into experimental or clinical development pathways.
This work is presented as a bioRxiv preprint by Dipanshu Ranjan Pattanayak and colleagues, posted September 14, 2026. The authors declared no competing interests in the preprint.