Molecular Structure and Pronounced Conformational Flexibility of Doxorubicin in Free and Conjugated State within a Drug–Peptide Compound

Abstract

The search for targeted drug delivery systems requires the design of drug-carrier complexes, which could both reach the malignant cells and preserve the therapeutic substance activity. A promising strategy aimed at enhancing the uptake and reducing the systemic toxicity is to bind covalently the drug to a cell-penetrating peptide. To understand the structure-activity relationship in such preparations, the chemotherapeutic drug doxorubicin was investigated by unrestrained molecular dynamics simulations, supported by NMR, which yielded its molecular geometry in aqueous environment. Furthermore, the structure and dynamics of a conjugate of the drug with a cell-penetrating peptide was obtained from molecular dynamics simulations in aqueous solution. The geometries of the unbound compounds were characterized at different temperatures, as well as the extent to which they change after covalent binding and whether/how they influence each other in the drug-peptide conjugate. The main structural fragments that affect the conformational ensemble of every molecule were found. The results show that the transitions between different substructures of the three compounds require a modest amount of energy. At increased temperature, either more conformations become populated as a result of the thermal fluctuations or the relative shares of the various conformers equalize at the nanosecond scale. These frequent structural interconversions suggest expressed conformational freedom of the molecules. Conjugation into the drug-peptide compound partially immobilizes the molecules of the parent compounds. Nevertheless, flexibility still exists, as well as an effective intra- and intermolecular hydrogen bonding that stabilizes the structures. We observe compact packing of the drug within the peptide that is also based on stacking interactions. All this outlines the drug-peptide conjugate as a prospective building block of a more complex drug-carrier system.

The self-association equilibria of doxorubicin at high concentration and ionic strength characterized by fluorescence spectroscopy and molecular dynamics simulations

“…Finally, the analysis of the DX structures as sampled by the 450 K MD simulations indicates that its internal degrees of freedom are not significantly affected by the dimer formation, i.e. the distributions of selected dihedral angles of the monomeric form -in line with a previous literature report [28] -do not change upon dimerization (see ESI - Figure S2).…”

Characterization of the interaction forces in a drug carrier complex of doxorubicin with a drug‐binding peptide

“…in aqueous solution. [8] We demonstrated the importance of hydrogen bonding between doxorubicin and the surrounding solvent molecules in its interaction with covalently attached peptide carriers like octaarginine. Overall, we could show that the geometries of DOX and peptide are not entirely rigid and several conformers are populated in water at room and body temperature.…”

“…The force field AMBER03 is used for the peptide, the drug, and the chloride anions. Full description of the parameters used for DOX is provided in our previous publication . Berendsen barostat and thermostat are employed for maintaining conditions as close as possible to the experimental ones—constant pressure of 1 bar, and two temperatures—25°C or 37°C.…”

“…Full description of the parameters used for DOX is provided in our previous publication. [8] Berendsen barostat and thermostat [21] are employed for maintaining conditions as close as possible to the experimental ones-constant pressure of 1 bar, and two temperatures-25°C or 37°C. The first one is the temperature of laboratory experiments and the second one-of the human body.…”

“…Molecular dynamics (MD) computations can be utilized to optimize drug delivery agents and to study the properties of the materials, such as their structure, stability, diffusion, and interactions in biological milieu . Recently, our group reported the first MD calculation of the structure and dynamics of a well‐known anthracycline chemotherapeutic (doxorubicin, DOX, Figure ) in aqueous solution . We demonstrated the importance of hydrogen bonding between doxorubicin and the surrounding solvent molecules in its interaction with covalently attached peptide carriers like octaarginine.…”