DNA MINOR-GROOVE RECOGNITION BY A TETRAHYDROPYRIMIDINIUM ANALOG OF HOECHST-33258 - NMR AND MOLECULAR-DYNAMICS STUDIES OF THE COMPLEX WITH D(GGTAATTACC)(2)

Hoechst 43254 (H43254), a 2,3,4,5-tetrahydropyrimidin-1-ium analogue o f the bis-benzimidazole minor groove binding agent Hoechst 33258 (H332 58), has been studied by NMR and restrained molecular dynamics in its complex with d(GGTAATTACC)(2). We investigate the origin of the enhanc ed complex stability afforded by the replacement of the N-methylpipera zine ring of H33258 with the tetrahydropyrimidinium ring of H43254, th e latter presenting the opportunity for specific minor groove-directed recognition through a pyrimidinium NH. A set of 25 drug-DNA NOEs defi ne the binding site with some precision and are used as part of the st ructural analysis using restrained molecular dynamics simulations cons idering explicit solvation and the treatment of electrostatic interact ions using the particle mesh Ewald method within AMBER 4.1. Starting w ith three different initial structures with the drug located at differ ent sites in the groove (pairwise RMSD 4.3-12.6 Angstrom) we arrive at three very similar structures (pairwise RMSD 0.80-1.34 Angstrom) repr esenting one converged binding site at the centre of the AATT tract. T wo of the three structures show the tetrahydropyrimidinium ring to be suitably positioned for an -NH to adenine N3 hydrogen bond suggesting that electrostatic interactions may play an important role in the enha nced affinity as well as imparting additional A-T specificity. The NMR data show that the pyrimidinium NH interaction is dynamic since signa l averaging from the two sides of the ring indicate rapid rotations in the bound form.