5H-8,9-Dimethoxy-5-(2-N,N-dimethylaminoethyl)dibenzo[c,h][ and ]naphthyridin-6-ones and related compounds as TOP1-Targeting agents: influence of structure on the ternary cleavable complex formation

In this paper, we present our results from a docking study of the title compounds with the DNA/topoisomerase I complex based on the recently published X-ray crystal structure of the topotecan/DNA/topoisomerase I ternary cleavable complex (Staker, B.L., et al. PNAS2002, 99, 15387) using the Autodock program. Simple intermolecular docking energies (Edock) correlate well with in vitro DNA cleavage data suggesting that the binding mode from the crystal structure is a reasonable binding mode for these compounds.