Molecular level insights into the inhibition of gene expression by thiamine pyrophosphate (TPP) analogs for TPP riboswitch: A well-tempered metadynamics simulations study

Abstract

Riboswitches are metabolite sensing aptamer domains present in non-coding regions in RNA and act as gene-regulating elements. Thiamine pyrophosphate (TPP) riboswitch is evolved as a new target for developing antibiotics against many pathogenic bacteria. The earlier reports suggest that the modification of the pyrophosphate group in the ligand molecule can enhance gene expression. In this work, we have examined the binding affinity and efficacy of TPP and two recently reported ligands, CH2-TPP, and CF2-TPP, using Well-tempered metadynamics (WT-MtD) simulations. The experimental in vitro assays show that both TPP and CH2-TPP repress the gene expression to the same extent. The calculated binding energies correlate well with the experimental study and show the same trend of binding affinity of ligands for the TPP riboswitch. The root mean square fluctuation profiles suggest that the CH2-TPP and TPP trigger higher fluctuations in P1 and L3 region, and such fluctuations in the P1 region is involved in the gene regulation process. The metal ion mediated contact of TPP ligand with pyrophosphate binding helix is found to be critical in the gene regulation process. The simulation results corroborate the experimental observations that the role of conformational changes occurring in different riboswitch regions upon ligand binding is essential to repress the gene expression process. This work sheds light on the subtle change in the ligand structure that can induce a more considerable impact on binding affinity and efficacy of ligands with riboswitch.