Inhibition of gene expression in human cells through small molecule-RNA interactions.

Area of Science:

• Molecular Biology
• Medicinal Chemistry
• Virology

Background:

• RNA-protein interactions are crucial for cellular processes like transcription and translation.
• The HIV-1 Tat protein interacts with the trans-activation responsive region (TAR) RNA to activate viral gene expression.
• Targeting this specific RNA-protein interaction presents a potential strategy for antiviral therapy.

Purpose of the Study:

• To isolate small molecules that bind selectively to TAR RNA.
• To evaluate the potential of these molecules in inhibiting HIV-1 gene expression.

Main Methods:

• Construction of an encoded combinatorial tripeptide library (24,389 members).
• On-bead screening to identify TAR RNA-binding tripeptides.
• In vitro binding studies and stereospecific discrimination assays.
• Assessment of Tat-mediated transcriptional activation inhibition in human cells.

Main Results:

• Identification of a family of heterochiral tripeptides with structure-specific binding to the TAR RNA bulge loop.
• Demonstration of stereospecific binding preferences for the best tripeptide ligand.
• The lead tripeptide suppressed Tat-mediated transcriptional activation with an IC(50) of approximately 50 nM.
• The identified tripeptide RNA ligands are cell-permeable, non-toxic, and inhibit gene expression by interfering with RNA-protein interactions.

Conclusions:

• Small tripeptide molecules can be effectively isolated to bind specific RNA structures like TAR RNA.
• These tripeptides demonstrate potential as cell-permeable inhibitors of HIV-1 gene expression by disrupting essential RNA-protein interactions.
• The findings support the development of novel RNA-targeting therapeutics for viral infections.