Affiliation: International University Bremen,Department of Computational Biology, Campus Ring 1, D-28759 Bremen,Germany
The exploration of new target structures for anti-bacterial agents is of importance due to the increasing emergence of bacterial strains that are resistant to current antibiotic treatments. Many biological processes involve active participation of RNA molecules. The awareness of RNA containing molecules as potential targets for anti-infective agents has so far lagged behind other biological structures such as proteins. Several natural products bind specifically to RNA structural motifs in bacterial ribosomes inhibiting important steps of protein synthesis. The recently determined three-dimensional structure of the large and small subunits of the bacterial ribosome and several other RNA molecules and RNA-ligand complexes can be helpful for the design of new or improved therapeutic agents. In addition, high throughput screening methods and computational virtual screening approaches have been increasingly applied for ligand design targeting bacterial and viral RNA structures. In the present article, recent progress on searching for compounds that specifically target RNA will be reviewed. An emphasis will be given on structure-based computational RNA drug design approaches.