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Development and application of computer-based methods in rational molecular design for targeting infectious diseases


In chemical biology small organic molecules are used as probes in order to analyse the function of proteins and to study the molecular details of biological processes. The interactions of these molecules and proteins form the essential basis whereby molecules and proteins need to have complementary secondary structures in order to fulfil a biological function. The molecules are often thereby referred to as keys and the compatible protein as lock („Schlüssel-Schloss-Prinzip“, Emil Fischer, 1894).

The molecular design, i.e. the discovery and optimization of bioactive molecules (i.e. the right key) is significantly supported by computer-based methods. There is, for example, the possibility of using virtual screening in order to search for new molecules with a certain biological activity, whereby an appropriate virtual library can contain up to 10 million molecules. If the function of molecules are know, one can thus search for molecules which have a similar shape and way of interaction. In this context it is assumed that similar molecules also have a similar function. However, knowing the three-dimensional structure of a protein one can search for molecules that fit exactly like a key into an existing binding pocket.

The workgroup deals with the application of computer-based methods in order to identify new molecules for combating infectious diseases on the one hand, but on the other hand, with the development of approaches which can generally be used in molecular design. For validating our designed inhibitors we are also using some wet lab work like protein expression, enzyme assay and rudimentary synthesis. A degree in computer science is not required for the application of these methods, however, as a scientist, you just need to have a certain curiosity in using computers.