Molecular recognition between a new pentacyclic acridinium salt and DNA sequences investigated by optical spectroscopic techniques, proton nuclear magnetic resonance spectroscopy, and molecular modeling

A pentacyclic acridine, 1H-2,3-dihydroindolizino[7,6,5-kl]acridinium chlori de (1), related in structure to tetra- and pentacyclic marine natural produ cts, has previously been shown to induce apoptosis in breast and non-small- cell lung tumor cell lines and shows significant differences in biological potency and antitumor profile from other intercalating agents based on the acridine framework. We report on the molecular recognition of the acridiniu m salt with DNA, quantified by optical spectroscopic methods, and have comp ared these results with the clinical agent amsacrine (m-AMSA). The results point to an intercalative association between 1 and G-C-rich sequences of D NA. We have synthesized a hexamer duplex d(ACGCGT)(2), presenting two poten tial 5'-GpG recipient sites, and have investigated in detail by NMR and mol ecular modeling methods the orientational preferences of 1, particularly wi th regard to the pyrrolidine ring system. On the basis of the intermolecula r nuclear Overhauser effect (NOE) data, four possible intercalation models were considered; no single model produced a significantly better fit than a ny of the others. The best fit to the experimental data was obtained by con sidering a dynamic equilibrium between the different intercalated orientati ons with the drug maximizing ct-overlap with the G-C base pairs at the inte rcalation site. We found little evidence for any degree of groove specifici ty imparted by the pyrrolidine ring. If these simulations have biological r elevance they suggest that, at most, the agent induces only a transitory ho t spot in the DNA which, evidently, is sufficient to be sensed by damage-re cognition mechanisms of the cell.