Natural Product Inhibition and Enzyme Kinetics Related to Phylogenetic Characterization for Bacterial Peptidyl-tRNA Hydrolase 1.

D Scott Strange,W Blake Holloway,Steven S Gaffin,Hana Mcfeeters,Robert L Mcfeeters,Jacob N Wisotsky,Meredyth D Kinsella

doi:10.3390/molecules26082281

D Scott Strange, W Blake Holloway + Show 5 more

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https://doi.org/10.3390/molecules26082281

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Abstract

With the relentless development of drug resistance and re-emergence of many pathogenic bacteria, the need for new antibiotics and new antibiotic targets is urgent and growing. Bacterial peptidyl-tRNA hydrolase, Pth1, is emerging as a promising new target for antibiotic development. From the conserved core and high degree of structural similarity, broad-spectrum inhibition is postulated. However, Pth1 small-molecule inhibition is still in the earliest stages. Focusing on pathogenic bacteria, herein we report the phylogenetic classification of Pth1 and natural product inhibition spanning phylogenetic space. While broad-spectrum inhibition is found, narrow-spectrum and even potentially clade-specific inhibition is more frequently observed. Additionally reported are enzyme kinetics and general in vitro Pth1 solubility that follow phylogenetic boundaries along with identification of key residues in the gate loop region that appear to govern both. The studies presented here demonstrate the sizeable potential for small-molecule inhibition of Pth1, improve understanding of Pth enzymes, and advance Pth1 as a much-needed novel antibiotic target.

Highlights

While the phylogenetic analysis focused on pathogenic bacteria, Pth1 from three relevant non-pathogenic bacterial species were included
While Clade 1 is strictly populated by Pth1 from Gramnegative bacteria, Pth1 from Gram-positive bacterial species populate
This report demonstrates the advantage of characterizing multiple homologs, spanning phylogenetic space in antibiotic development

Summary

Introduction

With the relentless development of drug resistance and re-emergence of many pathogenic bacteria, new antibiotics and new antibiotic targets are in critical need. Bacterial peptidyltRNA hydrolase (Pth1) is emerging as a promising new avenue for antibiotic development. Whereas Pth is essential in a vast majority of pathogenic bacteria [8,9], eukaryotes have redundant peptidyl-tRNA hydrolases that are structurally and mechanistically unrelated, yet complement Pth function [9,10]. Inhibiting the essential function of Pth in bacteria provides a new avenue for antibiotic development. Interrupting protein translation, but not affecting the ribosome, Pth inhibition has many advantages in regards to antibiotic development. Inhibition of protein biosynthesis is a proven antibiotic strategy employed by currently used therapeutics, such as aminoglycosides, tetracyclines, and macrolides which target the ribosome. Being a new target, Pth inhibitors will be effective against drug-resistant bacterial strains

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