Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases

Area of Science:

• Biochemistry
• Enzymology
• Drug Discovery

Background:

• Pathogenic microorganisms utilize cofactor-independent phosphoglycerate mutase (iPGM), distinct from human cofactor-dependent phosphoglycerate mutase (dPGM).
• iPGM's active site dynamically forms a unique cavity upon substrate binding, posing challenges for traditional drug screening.
• Understanding iPGM's structure-function relationship is crucial for developing selective inhibitors.

Purpose of the Study:

• To identify novel ligands targeting iPGM using an alternative screening approach.
• To characterize the inhibitory mechanism and selectivity of identified ligands.
• To explore the potential of macrocyclic peptides in overcoming small-molecule screening limitations.

Main Methods:

• Utilized an mRNA-display macrocyclic peptide library (>10^12 members) against nematode iPGM.
• Selected and enriched lariat-like peptide ligands.
• Performed functional assays to determine inhibition and selectivity.
• Determined the crystal structure of the iPGM-ligand complex.

Main Results:

• Identified and named novel ligands 'ipglycermides'.
• Demonstrated sub-nanomolar inhibition of iPGM with complete selectivity over dPGM.
• Elucidated an allosteric inhibition mechanism via crystal structure analysis.
• Observed ligand binding at the bi-domain interface, engaging the transition metal cluster.

Conclusions:

• Macrocyclic peptides can effectively target iPGM through unique allosteric mechanisms.
• The identified ipglycermides represent promising leads for antimicrobial drug development.
• This approach expands chemical diversity for challenging enzyme targets.
• The findings highlight the utility of macrocyclic peptides in overcoming limitations of traditional small-molecule screening.