Modulation of the Conformational Space of SARS‐CoV‐2 RNA Quadruplex RG‐1 by Cellular Components and the Amyloidogenic Peptides α‐Synuclein and hIAPP

Abstract

Given the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which particularly threatens older people with comorbidities such as diabetes mellitus and dementia, understanding the relationship between Covid-19 and other diseases is an important factor for treatment. Possible targets for medical intervention include G-quadruplexes (G4Qs) and their protein interaction partners. We investigated the stability and conformational space of the RG-1 RNA-G-quadruplex of the SARS-CoV-2 N-gene in the presence of salts, cosolutes, crowders and intrinsically disordered peptides, focusing on α-Synuclein and the human islet amyloid polypeptide, which are involved in Parkinson's disease (PD) and type-II diabetes mellitus (T2DM), respec-tively. We found that the conformational dynamics of the RG-1 G4Q is strongly affected by the various solution conditions. Further, the amyloidogenic peptides were found to strongly modulate the conformational equilibrium of the RG-1. Considerable changes are observed with respect to their interaction with human telomeric G4Qs, which adopt different topologies. These results may therefore shed more light on the relationship between PD as well as T2DM and the SARS-CoV-2 disease and their molecular underpinnings. Since dysregulation of G4Q formation by rationally designed targeting compounds affects the control of cellular processes, this study should contribute to the development of specific ligands for intervention.

Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex

“…Although the CD spectra of RG-1 in Na + and K + containing buffer (black lines in Figure 6 , panels C and D) exhibit the same general features, the intensities of the bands are different. In particular in the presence of Na + , the positive band is less intense with respect to that in K + , indicating that the RG-1 is not fully folded or, most likely, a population of (partially) unfolded conformers coexist, as also previously observed in single-molecule FRET experiments [ 34 ]. Indeed, the spectrum of the fully unfolded RG-1 recorded at 75 °C shows a positive band around 270 nm, which is less intense with respect to the same band at 25 °C (see Supplementary Figure S4 ).…”

“…However, a more likely explanation may be found in the details of the conformational dynamics of RG-1. It was previously shown that not all RG-1 molecules in Na + solution are fully folded in a parallel conformation [ 34 ]. Single-molecule FRET data are rather consistent with a significant fraction of (partially) unfolded (~50%) states also being present.…”

Amyloid peptides with antimicrobial and/or microbial agglutination activity

“…N-protein of SARS-CoV-2 plays an important role in controlling the replication and assembling of viruses, which is also an important target to fight against the virus. Mukherjee et al ( 2022 ) found the amyloid proteins hIAPP and α-Synuclein can stabilize the partial folded conformation and completely folded conformation of RG-1 G4Q (RNA-G-quadruplex formed by putative G-quadruplex forming sequence RG-1 which locates in the coding sequence region of SARS-CoV-2 nucleocapsid phosphoprotein), respectively. RG1 G4Q can inhibit the translation of mRNA of the SARS-CoV-2 N-protein (Zhao et al 2021 ).…”

Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review

“…Now, this is a rapidly developing research field. When we were almost finished with this review, Mukherjee et al reported modulation of the conformational space of RG-1 G4 in SARS-CoV-2 by cellular components and two amyloidogenic peptides, α-Syn and hIAPP, which are involved in Parkinson's disease and type-II diabetes [148] . These peptides stabilized RG-1 folding in a sequence-specific way, which was different from their interaction with human telomeric G4.…”