Docking and scoring for nucleic acid-ligand interactions: Principles and current status

Abstract

Nucleic acid (NA)-ligand interactions have crucial roles in many cellular processes and, thus, are increasingly attracting therapeutic interest in drug discovery. Molecular docking is a valuable tool for studying molecular interactions. However, because NAs differ significantly from proteins in both their physical and chemical properties, traditional docking algorithms and scoring functions for protein-ligand interactions might not be applicable to NA-ligand docking. Therefore, various sampling strategies and scoring functions for NA-ligand interactions have been developed. Here, we review the basic principles and current status of docking algorithms and scoring functions for DNA/RNA-ligand interactions. We also discuss challenges and limitations of current docking and scoring approaches.

Keywords: DNA/RNA–ligand complexes; DNA/RNA–ligand interactions; Molecular docking; Nucleic acid–ligand docking; Nucleic acid–ligand interactions; Scoring function.