Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA

Abstract

Molecular models of six anthracycline antibiotics and their complexes with 32 distinct DNA octamer sequences were created and analyzed using HINT (Hydropathic INTeractions) to describe binding. The averaged binding scores were then used to calculate the free energies of binding for comparison with experimentally determined values. In parsing our results based on specific functional groups of doxorubicin, our calculations predict a free energy contribution of -3.6 +/- 1.1 kcal x mol(-1) (experimental -2.5 +/- 0.5 kcal x mol(-1)) from the groove binding daunosamine sugar. The net energetic contribution of removing the hydroxyl at position C9 is -0.7 +/- 0.7 kcal x mol(-1) (-1.1 +/- 0.5 kcal x mol(-1)). The energetic contribution of the 3' amino group in the daunosamine sugar (when replaced with a hydroxyl group) is -3.7 +/- 1.1 kcal x mol(-1) (-0.7 +/- 0.5 kcal x mol(-1)). We propose that this large discrepancy may be due to uncertainty in the exact protonation state of the amine. The energetic contribution of the hydroxyl group at C14 is +0.4 +/- 0.6 kcal x mol(-1) (-0.9 +/- 0.5 kcal x mol(-1)), largely due to unfavorable hydrophobic interactions between the hydroxyl oxygen and the methylene groups of the phosphate backbone of the DNA. Also, there appears to be considerable conformational uncertainty in this region. This computational procedure calibrates our methodology for future analyses where experimental data are unavailable.

Figure 1

Structures of the six anthracycline antibiotics used in our studies, showing the differences in functional groups that are deficient in various compounds.

Figure 2

Stereo diagram of a HINT interaction map for the intercalation of doxorubicin with the CAGC base pair sequence of DNA, which displays, visually, the quality and magnitude of the various binding contacts involved in the interaction. The contour surfaces are color coded by interaction type at a constant map density value of ±75. Blue surfaces represent favorable polar interactions; red surfaces represent unfavorable polar interactions; green surfaces represent favorable hydrophobic interactions; magenta surfaces represent unfavorable hydrophobic interactions. The interatomic distance between the N3′ ammonium on the doxorubicin sugar ring and the carbonyl oxygen atoms of three surrounding base pairs of DNA is also indicated.

Figure 3

Stereo diagram of a HINT interaction map for the intercalation of hydroxydoxorubicin with the CAGC base pair sequence of DNA, which displays, visually, the quality and magnitude of the various binding contacts involved in the interaction. The contour surfaces are color coded by interaction type at a constant map density value of ±75. Blue surfaces represent favorable polar interactions; red surfaces represent unfavorable polar interactions; green surfaces represent favorable hydrophobic interactions; magenta surfaces represent unfavorable hydrophobic interactions. The interatomic distance between the N3′ ammonium on the doxorubicin sugar ring and the carbonyl oxygen atoms of three surrounding base pairs of DNA is also indicated.