There are many advantages to targeting RNA instead of proteins including sequence-specific binding, more sites accessible for interaction, selective inhibition, exploitation of multivalent interaction and more facile attack on drug resistance. RNA's link to genomics and bioinformatics also allows for increased discovery and specificity testing. Aminoglycosides and macrolides are RNA-targeting antibiotics that inhibit prokaryotic translation through interaction with the A-site ribosomal ribosome. Despite their benefits, the efficacy of these antibiotics is reduced due to bacterial resistance, oral inactivity, toxicity, and weak binding common to carbohydrates. Therefore, aminoglycoside-based analogs are currently being synthesized to circumvent these issues. To identify possible specific RNA interactions, a screening technique is being developed. Compounds of interest are linked to the surface of microtiter plates to which libraries of RNA sequences are added and then decoded using gene chip technology.
Figure 5A. Members of the aminoglycoside and macrolide families. These families of glycoconjugates target ribosomal RNA in prokaryotes disrupting RNA translation. (J. Am. Chem. Soc. (2000) 122, 5230; Angew. Chem. Int. Ed. (2001) 40, 3508)
Figure 5B. Site of aminoglycoside disruption of translation in prokaryotes. Binding of the aminoglycoside to the 16S ribosomal RNA disrupts protein biosynthesis giving the family its antibiotic nature. Box: A synthetic dimeric aminoglycoside developed to target the bacterial 16S A-site. (J. Am. Chem. Soc. (2000) 122, 5230)
Figure 5C. RNA binding analysis by using genomic and proteomic tools. Proteomics: Comparison of the proteome (visualized on a 2D gel, MW=molecular weight, PI=isoelectric point) before and after incubation of the cell with the molecule under investigation. A subsequent analysis of the affected proteins by MALDI (matrix-assisted laser-desorption ionization) mass spectrometry facilitates the identification of selective inhibitors of translation. Genomics: Labeling of the complete pool of RNA present in a cell (through reverse transcription and in vitro transcription labeling of the resulting cDNA) is used to detect the specific binding of small molecules to RNA.