Dynamical characterization and multiple unbinding paths of two PreQ₁ ligands in one pocket

Area of Science:

• Molecular Biology
• Biophysics
• Computational Chemistry

Background:

• Riboswitches regulate bacterial gene expression via small molecule binding.
• Class 1 preQ1 riboswitch aptamers are crucial models for RNA folding and antibiotic drug targets.

Purpose of the Study:

• To characterize the binding determinants of the preQ1-II riboswitch aptamer to preQ1 ligands.
• To provide insights for designing novel small molecule antibiotics.

Main Methods:

• Conducted 62.4 μs of conventional and enhanced-sampling molecular dynamics (MD) simulations.
• Performed binding free energy decomposition analysis.
• Utilized enhanced sampling simulations to reveal ligand unbinding pathways.

Main Results:

• Identified specific nucleotide interactions (G5, C17, C18, A30, A12, C31) with preQ1 ligands at alpha and beta sites.
• Demonstrated the critical role of Mg2+ ions in stabilizing the binding pocket and facilitating ligand binding.
• Revealed two distinct pathways for alpha site ligand unbinding, influenced by the beta site ligand's presence.
• Observed ligand-induced pre-organization of the riboswitch for ligand entry.

Conclusions:

• The study elucidates the molecular mechanisms of preQ1 riboswitch-ligand interactions.
• Findings offer valuable information for the rational design of potent and specific small molecule antibiotics targeting riboswitches.