Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression.

Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ riboswitches.

The 5-lipoxygenase/cyclooxygenase-2 cross-over metabolite, hemiketal E, enhances VEGFR2 activation and promotes angiogenesis.

Consecutive oxygenation of arachidonic acid by 5-lipoxygenase and cyclooxygenase-2 yields the hemiketal eicosanoids, HKE and HKD. Hemiketals stimulate angiogenesis by inducing endothelial cell tubulogenesis in culture; however, how this process is regulated has not been determined. Here, we identify vascular endothelial growth factor receptor 2 (VEGFR2) as a mediator of HKE-induced angiogenesis in vitro and in vivo.

Custom DNA Microarrays Reveal Diverse Binding Preferences of Proteins and Small Molecules to Thousands of G-Quadruplexes.

Single-stranded DNA (ssDNA) containing four guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their DNA-binding specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ∼15,000 potential G4 structures.

Chemical Modulation of Pre-mRNA Splicing in Mammalian Systems.

RNA splicing is a key component of gene expression and proteomic diversity in humans. The spliceosome assembles on and processes individual nascent pre-mRNA transcripts into distinct mature mRNAs that can code for different proteins. Splicing programs can be affected by somatic mutations and changes in response to exogenous stimuli.

HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction.

The primary oncogenic event in ∼85% of Ewing sarcomas is a chromosomal translocation that generates a fusion oncogene encoding an aberrant transcription factor. The exact genomic breakpoints within the translocated genes, and vary; however, in breakpoints typically occur within introns 7 or 8. We previously found that in Ewing sarcoma cells harboring intron 8 breakpoints, the RNA-binding protein HNRNPH1 facilitates a splicing event that excludes exon 8 from the - pre-mRNA to generate an in-frame mRNA.

Synthetic ligands for PreQ riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.

Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ riboswitch aptamers.

Targeting Mammalian Translational Inhibition with Tetracyclines.

In this issue of Cell Chemical Biology, Mortison et al. (2018) report an in-depth mechanistic study of targets of two different tetracyclines in mammalian cells. Unbiased chemoproteomics and RNA sequence mapping help identify specific ribosomal substructures bound by tetracyclines, providing insight into the therapeutic potential for tetracyclines in many diseases.

Total Synthesis and Biological Activity of the Arachidonic Acid Metabolite Hemiketal E.

The total synthesis of hemiketal E (HKE) has been accomplished using a gold(I)-mediated cycloisomerization followed by oxidation of the enol ether product to introduce a unique keto-hemiketal, the core structure of HKE. Synthetic hemiketal E reproduced biosynthetically derived HKE in the inhibition of human platelet aggregation.

Discovery of Inhibitors of MicroRNA-21 Processing Using Small Molecule Microarrays.

The identification of small molecules that bind to and perturb the function of microRNAs is an attractive approach for the treatment for microRNA-associated pathologies. However, there are only a few small molecules known to interact directly with microRNAs. Here, we report the use of a small molecule microarray (SMM) screening approach to identify low molecular weight compounds that directly bind to a pre-miR-21 hairpin.