2. Academic Validation
  3. Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways

Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways

  • Structure. 2025 Aug 5:S0969-2126(25)00261-8. doi: 10.1016/j.str.2025.07.013.
Marim M Barghash 1,  Mark F Mabanglo 1,  Samuel E Hoff 2,  Dmytro Brozdnychenko 3,  Keith S Wong 1,  Gursonika Binepal 4,  Philbert Ip 1,  Jiarui Shen 1,  Tomohiro Furukawa 5,  Hidekazu Katayama 6,  Vincent Trudel 7,  Joanne Tan 7,  Andrei K Yudin 7,  Scott D Gray-Owen 4,  Shohei Sakuda 8,  Robert A Batey 7,  Siavash Vahidi 3,  Massimiliano Bonomi 2,  Walid A Houry 9
Affiliations

Affiliations

  • 1 Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.
  • 2 Institut Pasteur, Université Paris Cité, CNRS UMR3528, Computational Structural Biology Unit, 75015 Paris, France.
  • 3 Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
  • 4 Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
  • 5 Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba-shi, Ibaraki 305-8642, Japan.
  • 6 Liberal Arts Center, Teikyo University, 1-1 Toyosatodai, Utsunomiya-shi, Tochigi 320-8551, Japan.
  • 7 Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
  • 8 Department of Biosciences, Faculty of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya-shi, Tochigi 320-8551, Japan.
  • 9 Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada. Electronic address: walid.houry@utoronto.ca.
PMID: 40795847 DOI: 10.1016/j.str.2025.07.013
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.

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