Molecular basis for anticancer drug amplification: interaction of phleomycin amplifiers with DNA.

The interaction of two phleomycin amplifiers, N,N-dimethyl-2-[[4'-(thien-2''-yl)pyrimidin-2'-yl]thio]ethylamine (1S, high activity) and N-[2''-(dimethylamino)ethyl]-4-(thien-2'-yl)pyrimidin-2-amine (1N, low activity) with DNA has been evaluated. The visible absorption bands of both compounds shift to longer wavelengths, and both exhibit hypochromicity on titration with DNA. The effects for 1S at low concentration are significantly greater than for 1N. 1S increases the DNA Tm by 2.5 degrees C while 1N causes only a 1.0 degree C increase under the same conditions. Spectrophotometric binding analysis of the interaction of 1S and 1N with calf thymus DNA indicates that 1S binds over 4 times more strongly to this DNA than 1N. Both compounds increase DNA viscosity, cause downfield shifts in DNA 31P NMR spectra, and shift the DNA imino base pair protons upfield, conclusively demonstrating that they bind to DNA by intercalation. Signals for the aromatic protons of 1S and 1N are shifted upfield on addition of DNA as expected for intercalation. The shifts for all aromatic protons are similar on 1S and on 1N, indicating that both the pyrimidine and thiophene are inserted between the DNA base pairs in the complex. NOE experiments demonstrate that the compounds are in the s-cis conformation both free in solution and in the DNA intercalation complex. Semiempirical INDO/S calculations indicate greater polarization of the pi-electron system of 1S than 1N. This greater polarization may account for the stronger interaction of 1S with DNA base pairs than 1N. The interaction of these compounds with DNA is strongly correlated with their biological amplification activity.