Competitive Microarray Screening Reveals Functional Ligands for the DHX15 RNA G-quadruplex

Abstract

AbstractRNAs are increasingly considered valuable therapeutic targets, and in turn the development of methods to identify and validate both RNA targets and RNA-binding compounds is more important than ever. In this study, we utilized a bioinformatic approach to identify a hairpin-containing RNA G-quadruplex (rG4) in the 5′UTR ofDHX15mRNA. By using a competitive small molecule microarray (SMM) approach, we identified a compound that specifically binds to theDHX15rG4 with a KDof 12.6 ± 1 µM. This rG4 directly impacts translation of aDHX15reporter mRNAin vitro, and binding of our compound (F1) to the structure inhibits translation up to 57% with an IC50of 22.9 ± 3.8 µM. The DHX15 protein is an “undruggable” helicase associated with several types of cancer progression, and our data represent the first published effort to target the rG4 inDHX15mRNA to inhibit its translation. Overall, our work is informative for the development of novel small molecule cancer therapeutics for RNA targets starting from target identification.Graphical Abstract