In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction

Abstract

After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.

Multifaceted Aspects of HIV-1 Nucleocapsid Inhibition by TAR-Targeting Peptidyl-Anthraquinones Bearing Terminal Aromatic Moieties

“…The outcome of each competition was determined by ESI-MS under native conditions, a method shown for enabling the simultaneous detection of non-covalent binary complexes between RNA and NC and of nucleic acid-protein–ligand ternary complexes [ 16 ]. Control experiments were performed by incubating equimolar amounts of full-length NC protein with TAR construct in the absence of compound, which confirmed the formation of stable 1:1 TAR•NC complexes [ 16 , 35 ]. Representative spectra obtained from a mixture of equimolar concentration of NC and ligand-pretreated TAR (10 μM) are reported in Figure 5 and Figure S5 .…”