title: Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases.
abstract: Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >1012members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.
authors.affiliation: Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
authors.forename: Hao
authors.initials: H
authors.lastname: Yu
authors.affiliation: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Dranchak
authors.affiliation: Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA.
authors.forename: Zhiru
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: MacArthur
authors.affiliation: National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Munson
authors.affiliation: Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA.
authors.forename: Nurjahan
authors.initials: N
authors.lastname: Mehzabeen
authors.affiliation: National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Nathan J
authors.initials: NJ
authors.lastname: Baird
authors.affiliation: IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA.
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Battalie
authors.affiliation: National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
authors.forename: David
authors.initials: D
authors.lastname: Ross
authors.affiliation: Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Lovell
authors.affiliation: Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA.
authors.forename: Clotilde K S
authors.initials: CK
authors.lastname: Carlow
authors.affiliation: Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Suga
authors.affiliation: National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA.
authors.forename: James
authors.initials: J
authors.lastname: Inglese
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001419:Bacteria / Q000201:enzymology*; D055162:Biocatalysis / Q000187:drug effects; D017173:Caenorhabditis elegans / Q000201:enzymology; D003067:Coenzymes / Q000378:metabolism; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000494:pharmacology*; D047028:Macrocyclic Compounds / Q000737:chemistry / Q000494:pharmacology*; D008958:Models, Molecular; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D010736:Phosphoglycerate Mutase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D010802:Phylogeny; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013438:Sulfhydryl Compounds / Q000378:metabolism
chemical_list: D003067:Coenzymes; D004791:Enzyme Inhibitors; D047028:Macrocyclic Compounds; D010455:Peptides; D013438:Sulfhydryl Compounds; D010736:Phosphoglycerate Mutase; D003545:Cysteine