Computerized selection of potential DNA binding compounds.

Abstract

Using a general shape-search docking algorithm, potential DNA minor groove binding compounds were selected from a subset from the Cambridge Crystallographic Database consisting of almost 10,000 molecules. The crystal structure of the DNA dodecamer as observed in the d(CGCGAATTCGCG)2.netropsin complex served as the target receptor. Surprisingly, the highest scoring compound turned out to be CC-1065, a potent anti-tumour agent. Netropsin itself was number 6 on the list of highest scoring compounds. A number of the top-10 scoring compounds may serve as a source of inspiration for further drug design.