Novel metabolite analogues for modulating riboswitch activity

Riboswitches are RNA elements mostly found in the 5' UTR of bacterial mRNA. Consisting of a metabolite-binding aptamer domain and an expression domain, they are involved in the regulation of up to 2-4% of all bacterial genes, and therefore have become a new target for developing antibiotics. For example, the expression of the enzyme which catalyses the synthesis of glucosamine-6-phosphate, an important metabolite of bacterial cell wall biosynthesis, is tightly regulated by the glmS riboswitch. In H. influenza and other pathogenic bacteria thi-box ribowitches have been shown to be involved in the regulation of essential genes. Interference with the orderly expression of those genes may enable control of bacterial growth. Therefore, we sought to identify modulators for these riboswitches based on structural analogy to their natural ligand. We designed and synthesized small libraries of metabolite analogues and investigated them regarding their activation of the glmS ribozyme of S. aureus or the E.coli thiM riboswitch. While the glmS ribozyme is activated by a carba-sugar in comparable levels to the natural metabolite GlcN6P, the thi-box riboswitch is modulated by a novel triazolethiamine compound in vivo. Moreover, activation by thriazolethiamine was shown to be more effective than by pyrithiamine, a known artificial thi-box activator.
Investigating riboswitches and their artificial regulation might allow encountering the increasing appearance of multi-resistant pathogenic strains, which seriously threatens our ability to control many microbial pathogens.