Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.
Thiamine pyrophosphate (TPP) riboswitches regulate essential genes in bacteria by changing conformation upon binding intracellular TPP. Previous studies using fragment-based approaches identified small molecule "fragments" that bind this gene-regulatory mRNA domain. Crystallographic studies now show that, despite having micromolar Kds, four different fragments bind the TPP riboswitch site-specifically, occupying the pocket that recognizes the aminopyrimidine of TPP. Unexpectedly, the unoccupied site that would recognize the pyrophosphate of TPP rearranges into a structure distinct from that of the cognate complex. This idiosyncratic fragment-induced conformation, also characterized by small-angle X-ray scattering and chemical probing, represents a possible mechanism for adventitious ligand discrimination by the riboswitch, and suggests that off-pathway conformations of RNAs can be targeted for drug development. Our structures, together with previous screening studies, demonstrate the feasibility of fragment-based drug discovery against RNA targets.
National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Katherine Deigan
KD
Warner
Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
Philip
P
Homan
Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
Kevin M
KM
Weeks
Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
Alison G
AG
Smith
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Chris
C
Abell
National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA. Electronic address: adrian.ferre@nih.gov.
Adrian R
AR
Ferré-D'Amaré
D001665:Binding Sites; D018360:Crystallography, X-Ray; D055808:Drug Discovery; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D012313:RNA / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results; D058928:Riboswitch; D013379:Substrate Specificity; D013835:Thiamine Pyrophosphate / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*
D008024:Ligands; D058928:Riboswitch; D012313:RNA; D013835:Thiamine Pyrophosphate