Tetraphenylethene Derivatives Modulate the RNA Hairpin-G-quadruplex Conformational Equilibria in Proto-Oncogenes

Targeting Two-Tetrad RNA G-Quadruplex in the SARS-CoV-2 RNA Genome Using Tetraphenylethene Derivatives for Antiviral Therapy

Targeting the specific RNA conformations that are crucial for SARS-CoV-2 replication is a viable antiviral approach. The SARS-CoV-2 genome contains GG repeats capable of forming unstable two-tetrad G-quadruplex (GQ) structures, which exist as a mix of conformations, including hairpin (Hp), intra-, and intermolecular GQs. RGQ-1, originating from the nucleocapsid gene's ORF, adopts a dynamic equilibrium of conformations, including intramolecular hairpin and G-quadruplex (Hp-GQ) structures, as confirmed by CD analysis. In this study, tetraphenylethene (TPE) derivatives were developed to target the Hp-GQ conformational equilibrium of RGQ-1. EMSA, fluorescence spectroscopy, and ITC assays confirmed that two TPE derivatives, TPE-MePy and TPE-Allyl Py, bind to RGQ-1. CD thermal melting experiments indicate that RGQ-1 is stabilized by 8.56 and 12.54 °C in the presence of TPE-MePy and TPE-Allyl Py, respectively. Additionally, luciferase assays demonstrated that TPE derivatives suppressed luciferase activity by 2.2-fold and 3.6-fold, respectively, shifting the HpGQ equilibrium toward the GQ conformation, as suggested by CD spectroscopy. Treatment of SARS-CoV-2-infected A549 cells with TPE derivatives reduced the levels of viral RNA, spikes, and nucleocapsid proteins. To explore their antiviral mechanism, preinfection and postinfection treatments were tested, revealing that the TPE derivatives specifically suppressed the postentry stages of viral replication without affecting viral entry. These findings highlight the therapeutic potential of TPE derivatives in inhibiting key gene expressions critical for SARS-CoV-2 replication.

A sodium/potassium switch for G4-prone G/C-rich sequences

Metal ions are essential components for the survival of living organisms. For most species, intracellular and extracellular ionic conditions differ significantly. As G-quadruplexes (G4s) are ion-dependent structures, changes in the [Na+]/[K+] ratio may affect the folding of genomic G4s. More than 11000 putative G4 sequences in the human genome (hg19) contain at least two runs of three continuous cytosines, and these mixed G/C-rich sequences may form a quadruplex or a competing hairpin structure based on G-C base pairing. In this study, we examine how the [Na+]/[K+] ratio influences the structures of G/C-rich sequences. The natural G4 structure with a 9-nt long central loop, CEBwt, was chosen as a model sequence, and the loop bases were gradually replaced by cytosines. The series of CEB mutations revealed that the presence of cytosines in G4 loops does not prevent G4 folding or decrease G4 stability but increases the probability of forming a competing structure, either a hairpin or an intermolecular duplex. Slow conversion to the quadruplex in vitro (in a potassium-rich buffer) and cells was demonstrated by NMR. 'Shape-shifting' sequences may respond to [Na+]/[K+] changes with delayed kinetics.

Alternative RNA Conformations: Companion or Combatant

RNA molecules, in one form or another, are involved in almost all aspects of cell physiology, as well as in disease development. The diversity of the functional roles of RNA comes from its intrinsic ability to adopt complex secondary and tertiary structures, rivaling the diversity of proteins. The RNA molecules form dynamic ensembles of many interconverting conformations at a timescale of seconds, which is a key for understanding how they execute their cellular functions. Given the crucial role of RNAs in various cellular processes, we need to understand the RNA molecules from a structural perspective. Central to this review are studies aimed at revealing the regulatory role of conformational equilibria in RNA in humans to understand genetic diseases such as cancer and neurodegenerative diseases, as well as in pathogens such as bacteria and viruses so as to understand the progression of infectious diseases. Furthermore, we also summarize the prior studies on the use of RNA structures as platforms for the rational design of small molecules for therapeutic applications.