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

Yu, Hao; Dranchak, Patricia; Li, Zhiru; MacArthur, Ryan; Munson, Matthew S.; Mehzabeen, Nurjahan; Baird, Nathan J.; Battalie, Kevin P.; Ross, David; Lovell, Scott; Carlow, Clotilde K. S.; Suga, Hiroaki; Inglese, James

doi:10.1038/ncomms14932

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

Journal Article · Mon Apr 03 00:00:00 EDT 2017 · Nature Communications

DOI:https://doi.org/10.1038/ncomms14932· OSTI ID:1355041

Yu, Hao ^[1]; Dranchak, Patricia ^[2]; Li, Zhiru ^[3]; MacArthur, Ryan ^[2]; Munson, Matthew S. ^[4]; Mehzabeen, Nurjahan ^[5]; Baird, Nathan J. ^[6]; Battalie, Kevin P. ^[7]; Ross, David ^[8]; Lovell, Scott ^[5]; Carlow, Clotilde K. S. ^[3]; Suga, Hiroaki ^[1]; Inglese, James ^[2]

Univ. of Tokyo (Japan)
National Inst. of Health, Rockville, MD (United States)
New England Biolabs, Ipswich, MA (United States)
National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Univ. of Kansas, Lawrence, KS (United States)
Univ. of the Sciences, Philadelphia, PA (United States); National Inst. of Health (NIH), Bethesda, MD (United States)
Argonne National Lab. (ANL), Argonne, IL (United States)
National Inst. of Health (NIH), Bethesda, MD (United States)

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 >10¹² members. 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institute of General Medical Sciences; National Inst. of Health

Grant/Contract Number:: AC02-06CH11357; P30GM110761

OSTI ID:: 1355041

Journal Information:: Nature Communications, Vol. 8, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Cited by: 31 works

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

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