Microbes, not humans: exploring the molecular basis of Pseudouridimycin selectivity towards bacterial and not human RNA polymerase
- 110 Downloads
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.
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.
These findings would enhance the design of potent and selective drugs for broad-spectrum antimicrobial activity.
KeywordsBinding free energy Pseudouridimycin RNA polymerase selectivity Sequence alignment
The authors thank the College of Health Sciences, University of KwaZulu-Natal for their infrastructural and financial support. Likewise, we thank the Center for High Performance Computing, Cape-Town for providing computational resources.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Burgess RR, Erickson B, Gentry D et al (1987) In: Reznikoff WS (ed) Bacterial RNA polymerase subunits and genes in RNA polymerase and the regulation of transcription, vol 198. Elsevier, New York, pp 3–15Google Scholar
- Hayes JM, Archontis G (2012) MM-GB(PB)SA calculations of protein-ligand binding free energies. In: Molecular dynamics—studies of synthetic and biological macromolecules. InTechOpenGoogle Scholar
- Lee J, Borukhov S (2016) Bacterial RNA polymerase–DNA interaction: the driving force of gene expression and the target for drug action. Front Mol Biosci 3:73Google Scholar
- Machaba KE, Mhlongo NN, Dokurugu YM, Soliman ME (2017) Tailored-pharmacophore model to enhance virtual screening and drug discovery: a case study on the identification of potential inhibitors against drug-resistant Mycobacterium tuberculosis (3R)-hydroxyacyl-ACP dehydratases. Fut Med Chem 9:1055–1071CrossRefGoogle Scholar
- Sheppard C, James E, Barton G et al (2016) Is it easy to stop RNA polymerase? Cell Cycle 5:399–404Google Scholar
- Srivastava A, Degen D, Ebright YW, Ebright RH (2012) Frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in Staphylococcus aureus Google Scholar
- Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461Google Scholar
- Ventola CL (2015) The antibiotic resistance crisis: part 1: causes and threats. P T A peer-reviewed. J Formul Manag 40:277–283Google Scholar