Structure-based RNA-ligand design – chances & challenges

Targeting RNA with small molecules is an emerging field. However, screening strategies usually rely on HTS, FBDD or derivatization of a known ligand while structure-based design is still in its infancy. In our work we demonstrate the applicability of computational tools like molecular docking and molecular dynamic simulations for RNA-ligand design and the required modifications compared to protein-targeting approaches. Strategies to address challenges arising from protonation and tautomerization, desolvation, and target dynamics are discussed. [1]

With the gained knowledge, prospective virtual screenings were performed for two targets: the pre-queuosine-1 (preQ1) riboswitch and the hepatitis C virus internal ribosomal entry site (HCV IRES) subdomain IIa. For both targets, novel ligands were identified and confirmed using biophysical binding assays. [1,2] Lessons learned from these test cases highlighted the importance of proper model validation, screening library design and human pose inspection prior hit selection.

However, hit identification is only the first step of RNA-ligand design and hit-to-lead optimization often proofs to be challenging, especially for RNA-targets with low information content. [3] Over the years, several strategies to overcome affinity-cliffs were elucidated including ribonuclease targeting chimeras (RiboTACs) or the inclusion of intercalators (acridines), covalent traps (chlorambucil) and poly-cationic moieties (aminoglycosides). While all of these can be successful in improving on-target affinity, compromises usually have to be made in selectivity and permeability. In a systematic approach, we elucidated the impact of charged moieties on affinity, selectivity and binding kinetics to find the balance sweet-spot between these metrics for RNA-ligand development.