Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• RNA recognition motifs (RRMs) are crucial for gene expression regulation.
• Targeting dynamic RRM/RNA interfaces with small molecules presents a significant challenge in drug discovery.
• The U2AF2 splicing factor, with its flexible RRM structure, binds pre-mRNA polypyrimidine sequences.

Purpose of the Study:

• To elucidate the binding mode of the U2AF2 inhibitor NSC-194308.
• To understand the molecular basis of NSC-194308-induced pre-mRNA stabilization on U2AF2.
• To explore the applicability of dynamic docking for targeting flexible protein/RNA interfaces.

Main Methods:

• Application and benchmarking of static and dynamic docking approaches.
• Inference of plausible NSC-194308 binding poses to U2AF2.
• Analysis of molecular interactions driving pre-mRNA stabilization.

Main Results:

• Dynamic docking is essential for accurately assessing inhibitor binding to flexible RRM architectures.
• The study provides insights into the molecular mechanism of NSC-194308 action.
• NSC-194308 enhances pre-mRNA binding to U2AF2, selectively inducing leukemia cell death.

Conclusions:

• Dynamic effects must be considered when targeting plastic and modular protein/RNA interfaces.
• The findings offer a broadly applicable mechanism for developing therapeutics targeting protein/protein/RNA interactions.
• This approach can guide the discovery of novel drugs for selective RNA function modulation.