Riboswitches are
messenger RNA (
mRNA) domains that regulate gene function in response to the intracellular concentration of a variety of metabolites and second messengers. They control essential genes in many pathogenic bacteria, thus representing an inviting new class of biomolecular target for the development of
antibiotics and chemical-
biological tools. In this Account, we briefly review the discovery of
riboswitches in the first years of the 21st century and their ensuing characterization over the past decade. We then discuss the progress achieved so far in using
riboswitches as a focus for
drug discovery, considering both the value of past serendipity and the particular challenges that confront current researchers. Five mechanisms of gene regulation have been determined for
riboswitches. Most bacterial
riboswitches modulate either transcription termination or translation initiation in response to
ligand binding. All known examples of eukaryotic
riboswitches, and some bacterial
riboswitches, control gene expression by alternative splicing. The glmS
riboswitch, which is widespread in Gram-positive bacteria, is a
catalytic RNA activated by
ligand binding: its self-cleavage destabilizes the
mRNA of which it is part. Finally, one example of a trans-acting
riboswitch is known. Three-dimensional structures have been determined for representatives of 13 structurally distinct
riboswitch classes, providing atomic-level insight into their mechanisms of
ligand recognition. While cellular and viral RNAs have attracted widespread interest as potential
drug targets,
riboswitches show special promise due to the diversity of small-molecule recognition strategies that are on display in their
ligand-binding pockets. Moreover,
riboswitches have evolved to recognize small-molecule
ligands, which is unique among known structured
RNA domains. Structural and biochemical advances in the study of
riboswitches provide an impetus for the development of methods for the discovery of novel
riboswitch activators and inhibitors. Recent rational
drug design efforts focused on select
riboswitch classes have yielded a small number of candidate
antibiotic compounds, including one active in a mouse model of
Staphylococcus aureus infection. The development of high-throughput methods suitable for
riboswitch-specific
drug discovery is ongoing. A fragment-based screening approach employing equilibrium dialysis that may be generically useful has demonstrated early success.
Riboswitch-mediated gene regulation is widely employed by bacteria; however, only the
thiamine pyrophosphate-responsive
riboswitch has thus far been found in eukaryotes. Thus,
riboswitches are particularly attractive as targets for antibacterials. Indeed, antimicrobials with previously unknown mechanisms have been found to function by binding
riboswitches and causing aberrant gene expression.