Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States. Issue 4 (14th February 2020)

• Record Type: Journal Article
• Authors: Ganser, Laura R.; Kelly, Megan L.; Patwardhan, Neeraj N.; Hargrove, Amanda E.; Al-Hashimi, Hashim M.
• Is Part Of: Journal of molecular biology. Volume 432:Issue 4(2020)
• Page Start: 1297
• Page End: 1304
• Publication Date: 2020-02-14
• Subjects: RNA dynamics -- HIV-1 -- TAR -- ensemble -- drug discovery; ES excited conformational state -- GS ground state -- TAR transactivation response element -- RRE Rev response element -- wtTAR wild-type TAR -- RD relaxation dispersion -- ARG argininamide; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2019.12.009
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Many promising RNA drug targets have functions that require the formation of RNA-protein complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules. Regulatory RNAs have been shown to transiently form excited conformational states (ESs) that remodel local aspects of secondary structure. In some cases, the ES conformation has been shown to be inactive and to be poorly recognized by protein binding partners. In these cases, specifically targeting and stabilizing the RNA ES using a small molecule provides a rational structure-based strategy for inhibiting RNA activity. However, this requires that a small molecule discriminates between two conformations of the same RNA to preferentially bind and stabilize the short-lived low-abundance ES relative to the long-lived more abundant ground state (GS). Here, we tested the feasibility of this approach by designing a mutant that inverts the conformational equilibrium of the HIV-1 transactivation response element (TAR) RNA, such that the native GS conformation becomes a low-abundance ES. Using this mutant and NMR chemical shift mapping experiments, we show that argininamide, a ligand mimic of TAR's cognate protein binding partner Tat, is able to restore a native-like conformation by preferentially binding and stabilizing the transient and low-populated ES. A synthetic small molecule optimized to bind the TAR GS also partially stabilized the ES, whereas an aminoglycoside molecule that binds RNAs nonspecifically did not preferentially stabilize the ES to a similar extent. These results support the feasibility of inhibiting RNA activity using small molecules that preferentially bind and stabilize the ES. Graphical abstract: Image 1 Highlights: An HIV-1 TAR mutant was designed to invert the ground and excited state populations. Two structure-specific molecules stabilize the excited state of the TAR mutant. A non-specific molecule binds the TAR mutant without stabilizing the excited state. Stabilizing RNA excited states is a promising approach to inhibit RNA activity.