RNA: New Antimicrobial Strategies

National Heart, Lung, And Blood Institute

Investigators

Linked publications, trials & patents

Abstract

In the past year, we reported on successful structure-guided discovery of small molecules targeting the ZTP riboswitch. This bacterial regulator is an mRNA domain that responds to ZTP, which accumulates during folate stress. Collaborating with the Schneekloth laboratory (NCI) we performed both, unbiased and structure-guided searches for new small molecules that bind the regulatory RNA, and trigger its function, in vitro and in vivo. We discovered that replacing the ribose-phosphate moiety of ZTP with simple heterocycles results in less polar compounds that nonetheless bind and activate the ZTP riboswitch comparably to the cognate ligand. The best of our current compounds binds to the riboswitch with approximately three times higher affinity than ZTP. Co-crystal structures show that these compounds take advantage of stacking of their heterocycle moiety on a conserved purine nucleobase of the riboswitch. Notably, the effective concentration of these compounds is considerably higher than their dissociation constant, supporting other observations indicating that this regulator is under kinetic control. In addition to producing lead compounds for the future development of anti-RNA antibiotics, this works underscores the importance of functional screening, as equilibrium binding studies may not yield the most active small molecules.