Development of Antibiotic RNA Aptamers

New therapy approaches are needed to keep step with fast evolving strains of bacteria. My work aims to the development of RNA oligonucleotides as a new class of antibiotic substances. Short RNA molecules are able to form complex three dimensional structures, which bind targets with high specificity and high affinity. These RNA oligonucleotides are called aptamers and can be developed for binding to virtually any target, starting from small molecules, over proteins, up to whole cells. The development of RNA aptamers is performed through an evolutionary in vitro selection process, termed SELEX. For antibiotic purposes, RNA aptamers shall be selected, which bind and inhibit penicillin binding domains (pbd) or β-lactamases in the bacterial cell wall. The main criterion for aptamer binding is the surface structure of the target protein. We chose pdb structures of the β-lactamase and pbd family and clustered them according to surface characteristics. We used the program PIPSA, which performs a multiple protein alignment and compares the surface electrostatics using a grid based approach. We identified two clusters that are closely related to our first target TEM-1 and contain proteins derived from clinically relevant bacterial strains. Comparative binding studies of the TEM-1 aptamer with members of the identified target clusters are planned. We anticipate finding aptamers, which targets cluster members and thereby comprises antibiotic potential.