Discovery of Selective Ligands for Telomeric RNA G-quadruplexes (TERRA) through ¹⁹F-NMR Based Fragment Screening

Abstract

Telomeric repeat-containing RNA (TERRA) is a novel and very attractive antitumoral target. Here, we report the first successful application of (19)F-NMR fragment-based screening to identify chemically diverse compounds that bind to an RNA molecule such as TERRA. We have built a library of 355 fluorinated fragments, and checked their interaction with a long telomeric RNA as a target molecule. The screening resulted in the identification of 20 hits (hit rate of 5.6%). For a number of binders, their interaction with TERRA was confirmed by (19)F- and (1)H NMR as well as by CD melting experiments. We have also explored the selectivity of the ligands for RNA G-quadruplexes and found that some of the hits do not interact with other nucleic acids such as tRNA and duplex DNA and, most importantly, favor the propeller-like parallel conformation in telomeric DNA G-quadruplexes. This suggests a selective recognition of this particular quadruplex topology and that different ligands may recognize specific sites in propeller-like parallel G-quadruplexes. Such features make some of the resulting binders promising lead compounds for fragment based drug discovery.

19F-labeling of the adenine H2-site to study large RNAs by NMR spectroscopy

“…peptide nucleic acid building blocks but also in ligand screening by NMR spectroscopy (Garavis et al 2014;Kiviniemi et al 2013).…”

Structure-Based Discovery of Small Molecules Binding to RNA

“…The suitability of FBDD for the discovery of telomeric RNA G-quadruplexes (TERRA) ligands was also demonstrated [122]. A library of 355 fluorinated fragments was screened by 19 F-NMR.…”

“…K D -values in the range of 120-1900 μM were reported with hit 8 (Fig. 7) displaying the highest affinity [122]. Surface plasmon resonance (SPR)-based biosensor assay methods are a useful tool to directly measure macromolecule-ligand interactions by determining binding affinities and kinetic parameters at the same time [123].…”

RNA Structures as Mediators of Neurological Diseases and as Drug Targets

“…High-resolution structures of ribosomes and other RNA-protein complexes combined with modeling of RNA dynamics have enabled structure-based approaches to develop new antibiotics and antivirals. Such studies have also enabled a fragment-based approach to drug design (Garavís et al, 2014). We recently reported a computational approach to design small molecules that bind RNA named Inforna (Velagapudi et al, 2014).…”