Modeling topoisomerase-DNA interactions and design of trapping inhibitors used for cancer

Abstract

Topoisomerase inhibiting chemotherapy is most appropriate in cancers containing high levels of topoisomerase. Study of these drugs is particularly difficult because two receptors, enzyme plus DNA, are involved. Genes of all three known human topoisomerases have neighboring oncogenes and those amplified receptors may be used to target topoisomerase inhibitors to transformed cells. To facilitate design of inhibitors, modeling tools of graphic imaging, sequence analysis, homology, molecular dynamics, energy evaluation, and QSAR were used. The principle findings are: (a) The widely accepted model of 5' attachment to DNA and 5' overhang is inconsistent with topoisomerase structure; 3' overhang is more likely. (b) The active site region near the catalytic tyrosine hydroxyl is well conserved between yeast and humans with some exceptions: 4 Å away Glu554->His566 is likely to modify the proton transport of the trans-esterification reaction conducted by this enzyme; two base pairs away, the yeast Asp 552 appears to probe the DNA major groove and becomes an oppositely charged Arg 565 in humans; 8-15 A away along the probable location of DNA backbone, the acid pair Glu-Asp 512-13 is conserved and repeated in humans as Glu-Asp-Glu-Asp (522-5); these residues might coordinate the required Mg2+ along with the conserved Asp 635 (644 in humans); the acidic triad 590-2 evolves to a hydroxy triad and might provide a proton transport pathway for the trans-esterification reaction. (c) Drug resistant mutant structure analysis suggests multiple sites of action on topoisomerase and suggests the region of DNA binding. (d) Prediction of intercalator binding to DNA is correctly ranked by molecular mechanics for amonafide and azonafide; however, there remains significant error from experimental cytotoxicity; force field error derives from the approximation of electron orbitals as van der Waals spheres, lack of polarization functions, poor handling of hydrogen bond variability, and force field parameterization from packed protein crystals. (e) Wide variability of the azonafide analogs on whole cell assays makes QSAR difficult and suggests other biochemical pathways are affected; the measurements need to be redone on a simple enzyme-DNA assay.