In the past year, efforts have centered on the glmS ribozyme-riboswitch and the thiamine pyrophosphate (TPP) riboswitch. The former is a catalytic RNA that controls synthesis of the bacterial cell wall in Gram-positive organisms. Previous crystallographic and biochemical work in our laboratory has demonstrated that glucosamine-6-phosphate (GlcN6P) functions as a coenzyme of the RNA. We have developed a synthetic chemistry program for the development of novel, unnatural GlcN6P analogs with better stability and potency than the natural metabolite. Although the synthetic chemistry of amine sugars is extremely challenging, we now have in hand several analogs of GlcN6P, putting us in a position to carry out systematic structure-activity relationship studies. The TPP riboswitch is widely distributed phylogenetically. Previously, our collaborator Dr. Abell and coworkers have carried out a fragment-based screen against this riboswitch and found a number of small organic molecules that bind with high specificity, albeit low affinity, to the RNA. Fragment-based screening is predicated on being able to elucidate the binding location of the low affinity fragments so that they can be elaborated into high affinity binders. Crystallographic work underway in our laboratory has confirmed the specificity of binding of a number of fragments, and elaboration of these into more potent ligands for the TPP riboswitch is underway. Part of this work is now in preparation for publication.

Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
National Heart, Lung, and Blood Institute
Zip Code
Warner, Katherine Deigan; Homan, Philip; Weeks, Kevin M et al. (2014) Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol 21:591-5
Baird, Nathan J; Ferre-D'Amare, Adrian R (2014) Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 1103:211-25
Zhang, Jinwei; Ferré-D'Amaré, Adrian R (2014) Dramatic improvement of crystals of large RNAs by cation replacement and dehydration. Structure 22:1363-71
Posakony, Jeffrey J; Ferre-D'Amare, Adrian R (2013) Glucosamine and Glucosamine-6-phosphate Derivatives: Catalytic Cofactor Analogues for the glmS Ribozyme. J Org Chem 78:4730-43