title: Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase.
abstract: Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC50 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC90 0.4 µg mL(-1) ). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.
authors.affiliation: Worldwide Research and Development, Pfizer Inc, Groton, Connecticut, 06340.
authors.forename: Dennis E
authors.initials: DE
authors.lastname: Danley
authors.forename: Eric T
authors.initials: ET
authors.lastname: Baima
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Mansour
authors.forename: Kimberly F
authors.initials: KF
authors.lastname: Fennell
authors.forename: Boris A
authors.initials: BA
authors.lastname: Chrunyk
authors.forename: John P
authors.initials: JP
authors.lastname: Mueller
authors.forename: Shenping
authors.initials: S
authors.lastname: Liu
authors.forename: Xiayang
authors.initials: X
authors.lastname: Qiu
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D000494:Allosteric Regulation / Q000187:drug effects; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology*; D018360:Crystallography, X-Ray; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D062105:Molecular Docking Simulation; D011008:Pneumococcal Infections / Q000188:drug therapy / Q000382:microbiology; D011106:Polyisoprenyl Phosphates / Q000378:metabolism; D012717:Sesquiterpenes / Q000378:metabolism; D013296:Streptococcus pneumoniae / Q000737:chemistry / Q000187:drug effects* / Q000201:enzymology* / Q000378:metabolism; D014166:Transferases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D011106:Polyisoprenyl Phosphates; D012717:Sesquiterpenes; C004808:farnesyl pyrophosphate; D014166:Transferases; D019883:Alkyl and Aryl Transferases; C106821:cis-prenyl transferase; C023266:undecaprenyl pyrophosphate synthetase
keywords: X-ray crystallography; antibiotic; cell wall; enzyme inhibitor; isopentenyl pyrophosphate chain; surface plasmon resonance; undecaprenyl pyrophosphate synthase