Proteins constitute the main group of molecular targets for most approved drugs. Moreover, more than 50% of drugs target proteins are derived from only four gene families: class I G protein-coupled receptors (GPCRs), nuclear receptors, ligand-gated ion channels and voltage-gated ion channels. The above facts make the prediction of protein structures and the design of ligands which modulate their activity an essential skill for a contemporary medicinal chemist. However, both medicinal chemistry and bioinformatics are often neglected in circulars for chemistry and pharmacy studies.
This article presents a proposal of computer classes on protein structure and function (10 hours), designated for the students of the third or fourth year of biology, chemistry or pharmacy. The course gets the students familiar with protein databases (eg. SwissProt and Protein Data Bank) as well as typical software for visualization of protein structures (eg. SPDBV, PyMol, Yasara). The participants get to know the diversity of proteins (GPCRs, ion channels, enzymes), learn how to analyze different levels of protein structures, to make a sequence alignment, to create a simple homology model and to analyze ligand-protein interactions. Most practical exercises concern the family of BCL-2 proteins which are apoptosis regulators.