Selective small-molecule inhibition of an RNA structural element

Abstract

Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.

The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

“…Similarly, our observation that a number of distinct azaaromatic compounds activate gene expression cannot be used as confirmation that the natural ligand or ligands for this riboswitch class can be classified as azaaromatic. It is possible to design and synthesize compounds that trick riboswitches into regulating gene expression by binding the natural ligand-binding pocket (Blount et al 2007(Blount et al , 2015Kim et al 2009;Mulhbacher et al 2010;Lünse et al 2011;Howe et al 2015). Therefore, the azaaromatic compounds that trigger gene expression in the current study might only be distal mimics of the natural target.…”

Riboswitch diversity and distribution

“…Indeed, efforts to create novel compounds that bind riboswitches have yielded antibacterial efficacy (Kim et al 2009;Mulhbacher et al 2010;Blount et al 2015;Howe et al 2015), although some of these compounds might use broader mechanisms to inhibit bacterial growth (Kim et al 2009;Kofoed et al 2016). The distribution of riboswitches among various divisions of bacteria (Fig.…”

Disciplined approach to drug discovery and early development

“…Moreover, phenotypic screens can be used to uncover unexpected mechanisms by which small molecules modulate a target or pathway (such as by binding to and modifying a regulatory RNA structure) (24). Further, beyond small molecules and monoclonal antibodies, new therapeutic modalities are gaining traction, such as mRNA delivery, small interfering RNA and antisense oligonucleotides, gene editing with CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9, and peptides.…”