Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of Na+ and K

by Selleckchem | Jun 10 2023

Rhinoviruses (RVs) are the major cause of common cold, a respiratory disease that generally takes a mild course. However, occasionally, RV infection can lead to serious complications in patients debilitated by other ailments, e.g., asthma. Colds are a huge socioeconomic burden as neither vaccines nor other treatments are available. The many existing drug candidates either stabilize the capsid or inhibit the viral RNA polymerase, the viral proteinases, or the functions of other non-structural viral proteins; however, none has been approved by the FDA. Focusing on the genomic RNA as a possible target for antivirals, we asked whether stabilizing RNA secondary structures might inhibit the viral replication cycle. These secondary structures include G-quadruplexes (GQs), which are guanine-rich sequence stretches forming planar guanine tetrads via Hoogsteen base pairing with two or more of them stacking on top of each other; a number of small molecular drug candidates increase the energy required for their unfolding. The propensity of G-quadruplex formation can be predicted with bioinformatics tools and is expressed as a GQ score. Synthetic RNA oligonucleotides derived from the RV-A2 genome with sequences corresponding to the highest and lowest GQ scores indeed exhibited characteristics of GQs. In vivo, the GQ-stabilizing compounds, pyridostatin and PhenDC3, interfered with viral uncoating in Na+ but not in K+-containing phosphate buffers. The thermostability studies and ultrastructural imaging of protein-free viral RNA cores suggest that Na+ keeps the encapsulated genome more open, allowing PDS and PhenDC3 to diffuse into the quasi-crystalline RNA and promote the formation and/or stabilization of GQs; the resulting conformational changes impair RNA unraveling and release from the virion. Preliminary reports have been published.

Comments:

That's an interesting summary of a research project focused on investigating the potential of G-quadruplex (GQ) structures in inhibiting the replication cycle of rhinoviruses (RVs). RVs are a major cause of the common cold, and while they usually result in mild symptoms, they can lead to complications in individuals with underlying conditions like asthma.

The lack of effective vaccines and treatments for the common cold has been a socioeconomic burden. Existing drug candidates have targeted various viral components, such as the capsid, viral RNA polymerase, and viral proteinases. However, none of these candidates have been approved by the FDA.

In this particular study, the researchers explored the possibility of targeting the genomic RNA of RVs by stabilizing RNA secondary structures, particularly G-quadruplexes. G-quadruplexes are formed by guanine-rich sequences that stack on top of each other, creating planar guanine tetrads through Hoogsteen base pairing. Certain small molecules can increase the energy required for unfolding G-quadruplex structures.

The researchers used bioinformatics tools to predict the propensity of G-quadruplex formation, expressed as a GQ score, in synthetic RNA oligonucleotides derived from the RV-A2 genome. They found that RNA sequences with the highest GQ scores exhibited characteristics of G-quadruplexes.

In in vivo experiments, two GQ-stabilizing compounds, pyridostatin (PDS) and PhenDC3, were tested. Interestingly, these compounds interfered with viral uncoating in Na+ (sodium ion) buffers but not in K+ (potassium ion) buffers. The researchers hypothesized that the presence of Na+ kept the encapsulated genome in a more open conformation, allowing PDS and PhenDC3 to diffuse into the RNA and promote the formation and/or stabilization of G-quadruplexes. These conformational changes impaired RNA unraveling and release from the virion.