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 (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced 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 VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS 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 VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA–ligand docking.

Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents

“…Finally, solvation and desolvation effects should also be considered upon ligand binding and water-mediated interactions. While explicit solvation sites within protein–ligand binding pockets can substantially impact affinity and selectivity, similar effects are likely represented in RNA–ligand binding sites as well [ 60 ].…”

Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6

“…Additionally, scoring was evaluated by docking SAM, SFG, and SAH and 150 decoys derived from the database of useful decoys-enhanced (DUD-E) [ 71 ] with similar physicochemical properties but distinct structural features. Even though FlexX is suitable for RNA-ligand docking [ 72 ], a docking setup without the tRNA present in the crystal structure was selected to allow potential ligands to not only bind to the SAM-, but also the Cyt-72 sub-pocket as demonstrated previously [ 25 ]. Additional interactions within this site hold the potential of improved binding affinity and selectivity while also interfering with tRNA binding.…”

Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications

“…5′-ends, or to modified nucleosides. 6,8–11 While this is effective to prevent steric interaction of the fluorophore with the investigated biomolecular interface, it might also reduce the effect of local structural changes (T-jump effects) on the dyes' fluorescence. 12,13…”