Structure and DNA binding activity of analogues of 1,5-bis(4-amidinophenoxy)pentane (pentamidine)

The DNA binding properties of a series of 39 bisbenzamidines related to the clinically used antipneumocystis drug pentamidine (1) were studied. Changes in the thermal denaturation temperature of calf thymus DNA (delta Tm) showed that all the compounds have significant affinity for DNA. A comparison of delta Tms for the series with delta Tms of base-pair-specific DNA-binding compounds, using homopolymers poly(dA).poly(dT) and poly(dG-dC).poly(dG-dC), indicated that the compounds show moderate specificity for AT base pairs. Lack of DNA helix extension, measured by viscometric titration with sonicated calf thymus DNA, indicated that the compounds do not bind to DNA by intercalation. Analogues of 1 with an odd number of methylenes connecting the benzamidine rings had a higher affinity for DNA and homopolymers than analogues with an even number of methylenes. All of the compounds containing an amidino group meta to the linking chain showed lower polynucleotide affinity. These results suggest that the shape of the molecules was important for DNA binding. Molecular modeling studies showed a correlation between the DNA binding and the radius of curvature of molecular mechanics models of the molecules. Monosubstitution on the benzamidine rings or replacement of the amidino group with the cyclic imidazolino group had no influence on the DNA-binding affinity of the compounds. Substitution of NH for the ether oxygen connecting group of 1 had no effect on the DNA binding or base-pair specificity. Methylation of either of the nitrogen atoms of the imidazolino group to provide an analogue of 1 with N-methylimidazolino groups decreased DNA affinity considerably. GC vs AT base-pair specificity as measured by delta Tm does not correlate with the radius of curvature. The experimental and modeling results are consistent with DNA minor-groove binding.