Microbes, not humans: exploring the molecular basis of Pseudouridimycin selectivity towards bacterial and not human RNA polymerase

Biotechnol Lett. 2019 Jan;41(1):115-128. doi: 10.1007/s10529-018-2617-1. Epub 2018 Oct 30.


Objective: Bacterial RNA polymerase (bRNAP) represent a crucial target for curtailing microbial activity but its structural and sequence similarities with human RNA polymerase II (hRNAPII) makes it difficult to target. Recently, Pseudouridimycin (PUM), a novel nucleoside analogue was reported to selectively inhibit bRNAP and not hRNAP. Till date, underlying mechanisms of PUM selectivity remains unresolved, hence the aim of this study.

Results: Using sequence alignment method, we observed that the β' of bRNAP and the RPB1 subunits of hRNAPII were highly conserved while the β and RPB2 subunits of both proteins were also characterized by high sequence variations. Furthermore, the impact of these variations on the differential binding of PUM was evaluated using MMPB/SA binding free energy and per-residue decomposition analysis. These revealed that PUM binds better to bRNAP than hRNAP with prominent bRNAP active site residues that contributed the most to PUM binding and stabilization lacking in hRNAPII active site due to positional substitution. Also, the binding of PUM to hRNAP was characterized by the formation of unfavorable interactions. In addition, PUM assumed favorable orientations that possibly enhanced its mobility towards the hydrophobic core region of bRNAP. On the contrary, unfavorable intramolecular interactions characterize PUM orientations at the binding site of hRNAPII, which could restrict its movement due to electrostatic repulsions.

Conclusion: These findings would enhance the design of potent and selective drugs for broad-spectrum antimicrobial activity.

Keywords: Binding free energy; Pseudouridimycin; RNA polymerase selectivity; Sequence alignment.

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Catalytic Domain
  • Humans
  • Nucleosides / analogs & derivatives*
  • Nucleosides / chemistry
  • RNA Polymerase II / chemistry*
  • RNA Polymerase II / genetics
  • Sequence Alignment*
  • Sequence Analysis, Protein*


  • Bacterial Proteins
  • Nucleosides
  • pseudouridimycin
  • RNA Polymerase II