Expedited approaches to the discovery and study of novel DNA binding ligands

Some of the most effective chemotherapeutic and anti-parasitic drugs target DNA. Our goal in this study is to rapidly identify new compounds that bind specifically to DNA to structurally characterize novel DNA-ligand complexes. Using a host-guest crystallographic method developed in our laboratory, we determined the 1.75 Å crystal structure of CD27, an antitrypanosomal, bound to DNA. This compound binds to DNA through bifurcated hydrogen-bonding within the minor groove, similar to classical minor groove binders and better than an analogue CD25. In further efforts, 60,000 compounds from the ChemDiv library were screened for DNA binding activity in the Chemical Genomics Core Facility Lab at IU School of Medicine. Using the high-throughput fluorescent intercalator displacement assay, the ability of compounds to displace ethidium bromide bound to calf thymus DNA was measured as a loss of fluorescence. From the screen, 165 compounds were identified that resulted in a 25% or greater decrease in fluorescence. Compounds identified in this screen vary in functionality and size, while retaining characteristics associated with known minor groove binders and intercalators. Validation of hits required an independent non-fluorescent assay in which 30 of the top compounds were confirmed to be DNA binders. Furthermore these compounds were characterized for their binding affinity to calf thymus DNA