Minor Groove of DNA as Target for Drug Design

In the recent years minor groove binding molecules have been found to influence DNA-dependent processes giving rise to an uncommon but very promising pathway for drug design: their affinity is high enough to prevent DNA binding enzymes from interaction with the DNA. Some of the minor groove binders can even be designed to target only specific DNA sequences. Thereby they are able to influence transcription control providing the possibility to systematically regulate the synthesis of proteins which take part in the course of diseases. Unfortunately, all highly sequence selective minor groove binders have the same scaffold, which includes a number of amide bonds and therefore lacks metabolic stability. Although the basic structural pattern of known ligands is always more or less the same, many slight variations of minor groove binding polypyrroles have been synthesized and subjected to detailed investigations. Therefore there is a great amount of data available, providing a firm basis for our project. We consider pharmacophore modeling methods to be the optimal tool to merge experimental data. This will lead to a deeper understanding of sequence specific properties of DNA-binding small molecules and to models able to reproduce the phenomenon. It will be a challenging task to adapt computational methods designed to describe protein-ligand interactions to the needs of DNA-ligand complex description. The resulting models will be used within virtual screening of libraries containing purchasable substances. Isothermal titration calorimetry (ITC) will help to validate and refine the pharmacophores which in a last step will be applied to virtual combinatorial library screening. This procedure promises new findings in the area of minor groove binding ligands. Our experience in the field of nucleic acid research combined with our experience in the field of pharmacophore modeling and virtual screening qualifies us optimally for this research.

Desoxyribonucleic acid DNA passes over genetic information from one generation to the next. Information is stored as base pairs in DNA, whereas the individual readout of information (genes) is controlled by DNA-binding proteins (transcription factors). Binding of transcription factors can be influenced by small molecule minor groove binders, binding directly to the minor groove of DNA in contrast to conventional drugs targeting proteins. Hence, DNA minor groove binders provide a novel and general way to treat genetic diseases, rendering the minor grove of DNA as target for drug design. Currently available DNA minor groove binders are derived from a narrow range of chemical scaffolds. These compounds suffer from low bioavailability and are therefore usually not considered in current drug design efforts. Thus, goal of the project was to overcome these limitations and to search for novel molecules binding to the minor groove of DNA. After thorough analyses of available structural data, computational similarity searches were carried out to identify novel DNA minor groove binder candidates based on available minor groove binders and their 3D structures, when bound to DNA. This was accomplished by pharmacophore-based search as well as shape- based virtual screening and validated with sets of known minor groove binders. Pharmacophore approaches were found highly successful in reproducing sequence specificity of known binders, whereas shape-based virtual screening was identified as perfectly suitable and rapid method to retrieve candidate molecules from large virtual molecule databases. In the course of the project several novel minor groove binders were identified and verified experimentally. Binding affinity was assessed by UV spectroscopy, minor groove binding by NMR spectroscopy. Isothermal titration calorimetry experiments were carried out to record thermodynamic profiles of minor groove binding leading to novel insights into sequence-specific DNA binding. These thermodynamic contributions were investigated by molecular dynamics simulations that shed further light on the connections between sequence- dependent DNA shape and binding characteristics. Especially, minor groove solvation was identified as a crucial point in the prediction of sequence-dependent DNA binding, which is followed up by further on-going projects in the group.