TY - JOUR

T1 - Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases

AU - Wiedmann, Mareike

AU - Dranchak, Patricia K

AU - Aitha, Mahesh

AU - Queme, Bryan

AU - Collmus, Christopher D

AU - Kashipathy, Maithri M

AU - Kanter, Liza

AU - Lamy, Laurence

AU - Rogers, Joseph M

AU - Tao, Dingyin

AU - Battaile, Kevin P

AU - Rai, Ganesha

AU - Lovell, Scott

AU - Suga, Hiroaki

AU - Inglese, James

N1 - Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

PY - 2021

Y1 - 2021

N2 - Human phosphoglycerate mutase (dPGM) catalysis is dependent on a 2,3-bisphosphoglycerate cofactor, while the nonhomologous isozyme in many parasitic species is cofactor-independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure-activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized C. elegans iPGM, measured as fold-enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using co-crystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from B. malayi, O. volvulus, D. immitis, and E. coli is achieved by a co-dependence between 1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ ion in the iPGM phosphatase domain, and 2) shape-complementarity surrounding the macrocyclic core at the phosphotransferase-phosphatase domain interface. Our results show that the high affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.

AB - Human phosphoglycerate mutase (dPGM) catalysis is dependent on a 2,3-bisphosphoglycerate cofactor, while the nonhomologous isozyme in many parasitic species is cofactor-independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure-activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized C. elegans iPGM, measured as fold-enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using co-crystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from B. malayi, O. volvulus, D. immitis, and E. coli is achieved by a co-dependence between 1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ ion in the iPGM phosphatase domain, and 2) shape-complementarity surrounding the macrocyclic core at the phosphotransferase-phosphatase domain interface. Our results show that the high affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.

U2 - 10.1016/j.jbc.2021.100628

DO - 10.1016/j.jbc.2021.100628

M3 - Journal article

C2 - 33812994

VL - 296

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

M1 - 100628

ER -