Investigation of the Role of Water in the Active Site of Viral Thymidin Kinases

Viral thymidine kinases (TKs) - especially HSV1-TK from Herpes Simplex Virus Type I - are not only the classical target of antiviral drugs, but are recently gaining importance as "suicide genes" in gene therapeutic approaches for the treatment of leukemia and other forms of cancer. For the further development of those concepts aiming on improved suicide gene/drug pairs molecular modelling methods are of major importance for the understanding of protein-ligand interactions. However, the treatment of HSV1-TK with those methods is difficult due to water molecules that are sequestered in the enzyme binding site in addition to the natural or synthetic ligand. These water molecules can easily be replaced by functional (e.g. OH) groups of the ligand or compensate for a group missing in the ligand or a mutant of the protein. While high-resolution X-ray structures usually allow to understand these effects qualitatively, their prediction is out of the scope of standard molecular modelling tools. The aim of the proposed research project is to develop general approaches for the modelling of the behaviour of water molecules sequestered in the binding pockets of proteins. Based on high-resolution X-ray structures of proteins containing water in their binding site, the properties of those water molecules will be studied with various molecular modelling methods of all levels of theory (force field, molecular dynamics, simulated annealing, quantum chemical calculations up to Car-Parinello ab-initio molecular dynamics), in order to identify common patterns and important effects influencing the interactions and binding energies of ligands and water molecules in the protein binding pocket. Finally, the knowledge gained in the preceding part of the project will be used to develop computational tools for the rapid generation of potential structures of protein-ligand-water complexes as well as estimation of their binding energy that can be used for instance in virtual library screening.