title: n-Alkylboronic acid inhibitors reveal determinants of ligand specificity in the quorum-quenching and siderophore biosynthetic enzyme PvdQ.
abstract: The enzyme PvdQ (E.C. 3.5.1.97) from Pseudomonas aeruginosa is an N-terminal nucleophile hydrolase that catalyzes the removal of an N-myristyl substituent from a biosynthetic precursor of the iron-chelating siderophore pyoverdine. Inhibitors of pyoverdine biosynthesis are potential antibiotics since iron is essential for growth and scarce in most infections. PvdQ also catalyzes hydrolytic amide bond cleavage of selected N-acyl-l-homoserine lactone quorum-sensing signals used by some Gram-negative pathogens to coordinate the transcription of virulence factors. The resulting quorum-quenching activity of PvdQ has potential applications in antivirulence therapies. To inform both inhibitor design and enzyme engineering efforts, a series of n-alkylboronic acid inhibitors of PvdQ was characterized to reveal determinants of ligand selectivity. A simple homologation series results in compounds with Ki values that span from 4.7 mM to 190 pM, with a dependence of ΔGbind values on chain length of -1.0 kcal/mol/CH2. X-ray crystal structures are determined for the PvdQ complexes with 1-ethyl-, 1-butyl-, 1-hexyl-, and 1-octylboronic acids at 1.6, 1.8, 2.0, and 2.1 Å resolution, respectively. The 1-hexyl- and 1-octylboronic acids form tetrahedral adducts with the active-site N-terminal Ser217 in the β-subunit of PvdQ, and the n-alkyl substituents are bound in the acyl-group binding site. The 1-ethyl- and 1-butylboronic acids also form adducts with Ser217 but instead form trigonal planar adducts and extend their n-alkyl substituents into an alternative binding site. These results are interpreted to propose a ligand discrimination model for PvdQ that informs the development of PvdQ-related tools and therapeutics.
authors.affiliation: Medicinal Chemistry Division, College of Pharmacy, †Biochemistry Graduate Program, and ⊥Center for Infectious Disease, The University of Texas , Austin, Texas 78712, United States.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Clevenger
authors.forename: Rui
authors.initials: R
authors.lastname: Wu
authors.forename: Dali
authors.initials: D
authors.lastname: Liu
authors.forename: Walter
authors.initials: W
authors.lastname: Fast
mesh_terms: D000581:Amidohydrolases / Q000037:antagonists & inhibitors / Q000737:chemistry*; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D001897:Boronic Acids / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011550:Pseudomonas aeruginosa / Q000201:enzymology*; D053038:Quorum Sensing; D017262:Siderophores / Q000096:biosynthesis*; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D001897:Boronic Acids; D008024:Ligands; D017262:Siderophores; D000581:Amidohydrolases; C438834:N-terminal nucleophile hydrolase