RNA is one of biology’s most versatile molecules. It carries genetic information, helps regulate gene expression and takes part in key cellular processes. This makes RNA an attractive target for drug discovery. Yet researchers still lack robust computational tools to predict how small molecules bind to RNA.
Filip Stefaniak, PhD, DSc Habil, from the Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology in Warsaw, aims to address this gap. His new NCN-funded project will develop DeepLeaRNA, a computational tool for predicting and explaining RNA–ligand binding.
Small-molecule ligands can bind RNA and modulate its structure and function, making RNA-ligand interactions a promising but underexploited target class in drug discovery. Understanding how and why a given ligand binds a specific RNA — its binding mode, pocket, and the structural determinants that govern it — is a critical early step in evaluating and designing compounds with potential biomedical or therapeutic relevance.“DeepLeaRNA will use advanced machine learning techniques and a and multiple molecular modeling methods to achieve accuracy and interpretability. It will provide insight into the molecular recognition process,” says Filip Stefaniak.
The project will focus not only on prediction, but also on explanation. This matters because researchers need to know more than whether a molecule may bind to RNA. They also need to understand why such binding is likely and which molecular features shape the interaction.
By making DeepLeaRNA available to the research community, the project may help accelerate studies in RNA biology and support the early stages of RNA-focused drug discovery.
For IIMCB, the grant expands research at the interface of RNA biology, bioinformatics, artificial intelligence and molecular medicine. It also builds on the Institute’s long-standing expertise in computational methods for RNA structure and interactions.
The project “Data-driven Methodology for Predicting, Explaining, and Understanding of RNA and Small Molecule Ligand Binding” received 1,458,376 PLN in funding under the OPUS 30 call.
Funding note
The project described in this article is funded by the National Science Centre, Poland: “Data-driven Methodology for Predicting, Explaining, and Understanding of RNA and Small Molecule Ligand Binding”, project no. 2025/59/B/NZ2/01768, OPUS 30.