Developing medicinal compounds capable of fighting antibiotic-resistant bacteria is a process that takes intense collaboration and, sometimes, one-of-a-kind equipment.
Professors Rob Batey and Walid A. Houry of the Department of Chemistry (Professor Houry’s main appointment is the Department of Biochemistry; he is cross-appointed to the Department of Chemistry) have been tackling this challenge together with their teams and other researchers for some years.
“My lab works on protein structure and biochemistry,” explained Professor Houry, who stated that a joint graduate student with Professor Batey--Funing Lin, who has since graduated--had begun one such research journey by making potential medicinal compounds as part of his PhD work.
Professor Batey’s group worked on the compound design and synthesis, while the Houry lab worked on the biochemical and structural characterization of compound binding to their target protein. Expanding the collaboration, the groups then worked with Professor Scott Gray-Owen’s lab at the Department of Molecular Genetics to test the effect of the compounds on different bacteria.
ClpP plays a crucial role in protein quality control, by degrading damaged or misfolded proteins, thereby maintaining cellular homeostasis. The compounds in question target ClpP, a protease enzyme that catalyzes the breakdown of proteins within living cells.
“Interestingly, the compounds act not as inhibitors but activators of the enzyme by binding to an allosteric regulation pocket. The compounds were designed using a rational design approach inspired by the binding modes of a related series of compounds,” explained Professor Batey.
As UofT laboratories were testing the new compounds against the protease ClpP and selected bacteria, additional samples were shipped to Saskatchewan for imaging at the Canadian Light Source synchrotron, a national research facility based at the University of Saskatchewan. Canada’s only synchrotron, the CLS that works by creating synchrotron radiation - bright and intense broad-spectrum light. When properly focused, the light allows researchers to investigate the properties of materials at the atomic and molecular levels. This can lead to advancements in fields like environmental science, materials engineering and, in this case, medicine.
“The use of the synchrotron really enabled us to visualize the orientation in which our bacterial-specific compounds were binding to bacterial ClpP and how that same orientation was likely not seen in human ClpP. That key insight drove the selectivity we saw and the potential risk-benefit profile we would need to achieve in a clinical antibiotic,” said Dr. Lin.
Houry noted that many bacteria have been able to develop resistance against clinically-relevant antibiotics. “There’s an urgent need to develop new antibiotics with a new mechanism of action.”
The new compounds were effective against two major pathogens: Neisseria meningitidis and Neisseria gonorrhoeae. The compounds work by dysregulating the activity of the ClpP protease within the cells of those bacteria. “It causes the protease to cleave proteins that are not supposed to be cleaved,” Houry said. “The dysregulated protease starts chewing up proteins in the bacterial cell unspecifically, which causes the death of the bacteria.”
The catch? Mammalian cells, like the targeted bacteria, also have ClpP. It was therefore important that the team show that Lin's compounds did not affect human ClpP—just the pathogens.
Long term collaborations of this nature are crucial to understanding complex problems like antibiotic resistance, and to developing effective solutions.
“This approach is great for developing novel antibiotics,” said Houry.
Related article: University of Saskatchewan synchrotron fighting drug resistant bacteria
Read the paper: Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases