Although many readers may have been excited about the release of the new Prince album last month, the biggest comeback story of this year was over at Nature. The antibiotic field has reported only covers or remixes since the 1980s, but now researchers from Merck pharmaceuticals have discovered a potential new antibiotic that works by targeting bacterial RNA.
Almost all drugs target enzymes, receptors or other proteins. But this is the era of deep sequencing, and the large repertoire of RNA in most genomes may represent an untapped source for drug discovery. Many RNAs are not conserved among species, so targeting them is likely to have few off target effects.
Take for example the bacterial riboswitch, a neat example of negative feedback regulation, in which metabolites control the expression of the set of enzymes that synthesize them. In bacteria, flavin mononucleotide (FMN), a metabolite produced from riboflavin (vitamin B12), binds to a riboswitch in the 5’UTR of mRNAs encoding genes involved in riboflavin biosynthesis. This regulates expression of the genes based on riboflavin abundance.
Bacteria, fungi and plants synthesize riboflavin (vitamin B12) whereas animals must acquire it from their diet. In theory, bacteria that cannot produce riboflavin could still thrive if the vitamin was present in their environment, but a few quick experiments using E.coli deletion mutants in a mouse infection model showed that these strains were poorly virulent. This suggested that blocking riboflavin biosynthesis impairs bacterial growth.
By high-throughput screening an internal library of 57,000 small molecules with antibacterial activity, the team identified a small molecule that they named ribocil, which suppressed bacterial growth only in the absence of riboflavin.
Ribocil appeared to act by interfering with the FMN riboswitch, because:
- Mutations in ribocil-resistant mutants mapped to the FMN riboswitch.
- When the FMN riboswitch was coupled to a GFP reporter gene, ribocil strongly inhibited GFP expression.
- A structure of ribocil bound to the FMN riboswitch determined by X-ray crystallography revealed that many resistance mutations mapped to the site of important contacts between ribocil and the riboswitch.
Finally, the team showed the potential of ribocil as an antibiotic. Ribocil is not a structural analog of FMN; therefore it could be administered in high doses and reduced bacterial burden by more than 1000 fold in a mouse model of E.coli septicemia.
With another potential antibiotic, teixobactin, discovered in January, it seems that 2015 may be the year of the antibiotic comeback.
Check out Nature, September 2015 for the full story.