Considerable evidence now indicates that aromatic systems with two terminal amidine or related groups can exhibit significant activity against a variety of opportunistic infection organisms. The groups of this NCDDG have invested considerable effort in analysis of the possible biological mechanism of these agents. Although much work remains to be done, several features that are essential for the activity of these compounds have emerged. First, minor-groove binding to the DNA of the organism is an essential requirement for an active compound. There are no active compounds that do not bind well to DNA. Second, activity and simple DNA binding are not directly correlated, and some additional agent is probably involved in the mechanism of action of the compounds. Third, nonspecific binding of the compounds to other DNA types and sequences as well as to RNA is correlated with toxic effects and should be minimized. The general goal of this core group is to conduct biophysical studies on the DNA complexes of drug candidates, prepared by the Boykin and Tidwell groups, and to use the information from the biophysical, biochemical, and biological testing studies, in combination with computer-based molecular modeling, to derive models for the drug-receptor complex. These models will be used to organize and interpret the experimental results, and to design new compounds for synthesis. The following specific steps will be taken to achieve the desired goals: An extensive data base of interaction strengths of all of the Boykin and Tidwell compounds with nucleic acids of different sequence and structure has been established during the first phase of this project, and the data base will be expanded with all new compounds from the synthetic groups. The information from these studies provides a first level of understanding of two key features of the interaction of these compounds with DNA: their general binding affinity and their level of sequence selectivity in binding. A key piece of information that is necessary for understanding the DNA interactions of the compounds is the DNA binding mode, particularly the sequence specificity of the binding mode. The compounds from the Boykin and Tidwell Groups that have good activity favor binding.in AT rich sequences of the DNA minor groove. We have found that relatively slight substituent modifications can convert minor-groove binding compounds into intercalators, threading intercalators, or external binding compounds. It appears that such dual binding modes might correlate with toxicity, and it is essential to evaluate the binding modes of all new compounds. To assist the computer modeling analysis of the interaction of the new drugs with DNA, high resolution 2D NMR and x-ray studies will be conducted on oligonucleotide complexes with drugs from different structural classes that show the most promising activity. The structural studies will be used to establish models for complexes of new drugs with DNA receptor sites. The final goal is to use the models derived from the experimental studies on the Boykin and Tidwell compounds along with known features of the minor-groove receptor site of DNA to design new compounds for synthesis.
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