title: Pyrrolamide DNA gyrase inhibitors: fragment-based nuclear magnetic resonance screening to identify antibacterial agents.
abstract: DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identified by a fragment-based lead generation (FBLG) approach using nuclear magnetic resonance (NMR) screening to identify low-molecular-weight compounds that bind to the ATP pocket of DNA gyrase. A pyrrole hit with a binding constant of 1 mM formed the basis of the design and synthesis of a focused library of compounds that resulted in the rapid identification of a lead compound that inhibited DNA gyrase with a 50% inhibitory concentration (IC(50)) of 3 μM. The potency of the lead compound was further optimized by utilizing iterative X-ray crystallography to yield DNA gyrase inhibitors that also displayed antibacterial activity. Spontaneous mutants were isolated in Staphylococcus aureus by plating on agar plates containing pyrrolamide 4 at the MIC. The resistant variants displayed 4- to 8-fold-increased MIC values relative to the parent strain. DNA sequencing revealed two independent point mutations in the pyrrolamide binding region of the gyrB genes from these variants, supporting the hypothesis that the mode of action of these compounds was inhibition of DNA gyrase. Efficacy of a representative pyrrolamide was demonstrated against Streptococcus pneumoniae in a mouse lung infection model. These data demonstrate that the pyrrolamides are a novel class of DNA gyrase inhibitors with the potential to deliver future antibacterial agents targeting multiple clinical indications.
authors.affiliation: Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts, USA. Ann.Eakin@astrazeneca.com
authors.forename: Ann E
authors.initials: AE
authors.lastname: Eakin
authors.forename: Oluyinka
authors.initials: O
authors.lastname: Green
authors.forename: Neil
authors.initials: N
authors.lastname: Hales
authors.forename: Grant K
authors.initials: GK
authors.lastname: Walkup
authors.forename: Shanta
authors.initials: S
authors.lastname: Bist
authors.forename: Alok
authors.initials: A
authors.lastname: Singh
authors.forename: George
authors.initials: G
authors.lastname: Mullen
authors.forename: Joanna
authors.initials: J
authors.lastname: Bryant
authors.forename: Kevin
authors.initials: K
authors.lastname: Embrey
authors.forename: Ning
authors.initials: N
authors.lastname: Gao
authors.forename: Alex
authors.initials: A
authors.lastname: Breeze
authors.forename: Dave
authors.initials: D
authors.lastname: Timms
authors.forename: Beth
authors.initials: B
authors.lastname: Andrews
authors.forename: Maria
authors.initials: M
authors.lastname: Uria-Nickelsen
authors.forename: Julie
authors.initials: J
authors.lastname: Demeritt
authors.forename: James T
authors.initials: JT
authors.lastname: Loch
authors.forename: Ken
authors.initials: K
authors.lastname: Hull
authors.forename: April
authors.initials: A
authors.lastname: Blodgett
authors.forename: Ruth N
authors.initials: RN
authors.lastname: Illingworth
authors.forename: Bryan
authors.initials: B
authors.lastname: Prince
authors.forename: P Ann
authors.initials: PA
authors.lastname: Boriack-Sjodin
authors.forename: Sheila
authors.initials: S
authors.lastname: Hauck
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: MacPherson
authors.forename: Haihong
authors.initials: H
authors.lastname: Ni
authors.forename: Brian
authors.initials: B
authors.lastname: Sherer
mesh_terms: D000577:Amides / Q000737:chemistry / Q000494:pharmacology*; D000818:Animals; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D027081:DNA Gyrase / Q000737:chemistry / Q000378:metabolism; D024881:Drug Resistance, Bacterial; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D006801:Humans; D020128:Inhibitory Concentration 50; D009682:Magnetic Resonance Spectroscopy; D051379:Mice; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D011758:Pyrroles / Q000737:chemistry / Q000494:pharmacology*; D013203:Staphylococcal Infections / Q000188:drug therapy / Q000382:microbiology; D013211:Staphylococcus aureus / Q000187:drug effects* / Q000235:genetics / Q000254:growth & development; D013296:Streptococcus pneumoniae / Q000187:drug effects* / Q000254:growth & development; D059005:Topoisomerase II Inhibitors
chemical_list: D000577:Amides; D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D011758:Pyrroles; D059005:Topoisomerase II Inhibitors; D027081:DNA Gyrase