Protein-based Virtual Screening Tools applied for RNA-Ligand Docking identify new Binders of the preQ₁-Riboswitch

Abstract

Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programmes to reproduce native binding modes of small molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programmes were found to perform similar compared to the RNA-based docking tool rDOCK and the faced challenges during docking, namely protomer and tautomer selection, target dynamics and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective virtual screening with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID and FlexX, followed by microscale thermophoresis assays identified 6 active compounds out of 23 tested virtual screening hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score, but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based virtual screenings against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.

Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives

“…Today, several RBP structures are available in apoform or in complex with nucleic acids, providing a robust starting point for applying this approach. Target-based virtual screening has also been applied to resolved RNA secondary structures to identify small molecules (Kallert et al, 2022). Finally, the fragment-based approach aims to test low-molecularweight molecules and generate candidate compounds from chemical fragments with low structural complexity and high chemical Frontiers in Molecular Biosciences frontiersin.org diversity.…”

Pose prediction accuracy in ligand docking to RNA

“…The success rates were evaluated for the docking programs with threshold RMSDs of 1.5 Å, 2.0 Å, and 2.5 Å relative to the crystal structure. A threshold RMSD of 2.5 Å was considered for evaluation of the performance/success rate of docking programs for RNA-ligand complexes as the ligand pockets in RNA tend to not be closed cavities and are less hydrophobic 25,[31][32][33] .…”

High-throughput competitive binding assay for targeting RNA with small molecules: discovery of new PreQ1riboswitch ligands

“…Development of synthetic ligands for the PreQ1 riboswitch able to suppress the production of proteins essential for Q synthesis and transport is of great interest for developing new antibiotics. Several PreQ1 analogues and synthetic ligands for the PreQ1 riboswitch have been discovered and investigated [27][28][29][30] , some of which are able to mimic PreQ1 function in in vitro and in vivo riboswitch assays. However, the discovery of new structurally diverse ligands of the PreQ1 riboswitch remains an interesting field of research.…”