Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways

Abstract

The bacterial ClpP protease is essential for the virulence and infectivity of many human pathogens and has emerged as a novel antibacterial drug target. Several classes of small molecules dysregulate or activate ClpP, leading to uncontrolled protein degradation and cell death. Here, we investigate the mechanism of ClpP activation by these compounds using an integrative approach combining structural, biochemical, and computational tools. We identified small molecules that activate ClpP through binding at internal catalytic sites where peptide bond hydrolysis occurs. Combined with knowledge of ClpP activation by small molecules that bind to external hydrophobic sites, this work sheds light on the mechanisms governing ClpP allostery and identifies a common molecular pathway utilized by site-specific effectors to achieve allosteric activation. We propose a consensus, bidirectional ClpP activation mechanism causing protease dysregulation.

Keywords: ClpP; Escherichia coli; Neisseria meningitidis; X-ray crystallography; activators of self-compartmentalizing proteases; boronic acids; dioctatin; drug design; hydrogen-deuterium exchange mass spectrometry; molecular dynamics simulations.