Structured viral RNA

Structured viral RNA refers to the complex secondary and tertiary folds within viral genomes, such as the HIV-1 Trans-activation response (TAR) element or the Hepatitis C Virus (HCV) Internal Ribosome Entry Site (IRES), which are essential for viral replication and protein synthesis (Hermann, 2016). These structures serve as critical scaffolds for the assembly of viral and host protein complexes, making them attractive therapeutic targets for small molecules and antisense oligonucleotides (Butcher & Pyle, 2011). By binding to these specific RNA motifs, drugs can sterically hinder essential interactions or stabilize non-functional conformations, thereby inhibiting the viral life cycle (Donlic & Hargrove, 2018). In the context of drug discovery, these well-characterized viral RNAs are often used as surrogates to study the selectivity and affinity of small molecules toward RNA in general. This approach helps in identifying chemical scaffolds capable of discriminating between different RNA structures, which is a major challenge in developing RNA-targeted therapies (Warner et al., 2018).

Other names

Viral RNA secondary structureStructured RNA motifsRNA regulatory elementsViral RNA tertiary structureRNA-targeted therapeutic motifs

Small molecule binding to specific RNA secondary or tertiary structures to sterically hinder protein-RNA interactions or induce conformational changes that inhibit viral replication or translation (Hermann, 2016; Donlic & Hargrove, 2018).