Modulation of the E. coli rpoH Temperature Sensor with Triptycene‐Based Small Molecules

Abstract

Regulation of the heat shock response (HSR) is essential in all living systems. In E. coli, the HSR is regulated by the alternative σ factor, σ32, which is encoded by the rpoH gene. The mRNA of rpoH adopts a complex secondary structure critical for proper translation of the σ32 protein. At low temperature the rpoH gene transcript forms a highly structured mRNA containing several three-way junctions, including a rare perfectly paired three-way junction (3WJ). This complex secondary structure serves as a primitive but highly effective strategy for thermal control of gene expression. Here, we report the first small molecule modulators of the E. coli σ32 mRNA temperature sensor.

Principles for targeting RNA with drug-like small molecules

“…Notably, these molecules were discovered using a wide variety of strategies that were intentionally focused on identifying RNA targets, and a subset are broadly drug-like, a feature emphasized by other recent reviewers 24 , 25 , 26 . Discovery strategies included high-throughput screening 30 , 32 , 36 , 37 , 38 , 39 , use of focused libraries 40 , 41 , 42 , structure-inspired design 43 , 44 , 45 , fragment-based approaches 46 and computational modelling 47 , 48 . Both compact and multivalent molecules are represented.…”

Insights into the development of chemical probes for RNA

“…This RNA element contains a rare, perfectly paired three-way junction that can be stabilized by symmetrical triptycene-based molecules, forming a distinct shape-selective fit ( 33 ). This stabilization resulted in an ∼60% reduction in translation of an σ 32 –GFP fusion protein and could potentially lead to antimicrobial activity ( 34 ). In addition, 7/41 chemical probes showed efficacy in animal models, targeting two RNA elements: r(CUG) exp repeats and pri-miRNA-96.…”

The Emerging Role of RNA as a Therapeutic Target for Small Molecules

“…Further work showed that diverse triptycene molecules can be synthesized in a modular and efficient fashion, including solid-phase methods that are likely to have use in the preparation of libraries of triptycenes going forward, with the potential for specific junction recognition ( Barros et al., 2016b , Yoon et al., 2016 ). Finally, a recent report demonstrated that functionalized triptycenes such as 8 ( Figure 1 D) can also be used to modulate the Escherichia coli rpoH RNA temperature sensor, indicating utility in recognizing RNA structures in bacteria as well ( Barros et al., 2016a ). To date, most of the work in this area has focused on molecular recognition and the development of synthetic methods to access new triptycene scaffolds; however, it is clear that this approach has potential for broad applications in RNA recognition and targeting in future efforts.…”

“…Structures of r(CUG) exp binding compounds 6 and 7 identified by high-throughput screening efforts are also shown (right) ( Childs-Disney et al., 2013 , Rzuczek et al., 2015 ). (D) Representative structure of a three-way junction (left) for which RNA-binding triptycene-based scaffolds such as compound 8 (right) were developed ( Barros et al., 2016a ). (E) Structure of the SARS-CoV RNA pseudoknot involved in an essential −1 ribosomal frameshift (left) used in a virtual screen to identify a SARS-pseudoknot-binding ligand (right) ( Park et al., 2011 ).…”

“… (D) Representative structure of a three-way junction (left) for which RNA-binding triptycene-based scaffolds such as compound 8 (right) were developed ( Barros et al., 2016a ). …”