title: 6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase.
abstract: BACKGROUND
  ATP-dependent D-alanine:D-alanine ligase (Ddl) is a part of biochemical machinery involved in peptidoglycan biosynthesis, as it catalyzes the formation of the terminal D-ala-D-ala dipeptide of the peptidoglycan precursor UDPMurNAc-pentapeptide. Inhibition of Ddl prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search of novel effective antimicrobial drugs. To address the problem of a relentless increase in resistance to known antimicrobial agents we focused our attention to discovery of novel ATP-competitive inhibitors of Ddl.
  
  
  RESULTS
  Encouraged by recent successful attempts to find selective ATP-competitive inhibitors of bacterial enzymes we designed, synthesized and evaluated a library of 6-arylpyrido[2,3-d]pyrimidine-based compounds as inhibitors of Escherichia coli DdlB. Inhibitor binding to the target enzyme was subsequently confirmed by surface plasmon resonance and studied with isothermal titration calorimetry. Since kinetic analysis indicated that 6-arylpyrido[2,3-d]pyrimidines compete with the enzyme substrate ATP, inhibitor binding to the ATP-binding site was additionally studied with docking. Some of these inhibitors were found to possess antibacterial activity against membrane-compromised and efflux pump-deficient strains of E. coli.
  
  
  CONCLUSIONS
  We discovered new ATP-competitive inhibitors of DdlB, which may serve as a starting point for development of more potent inhibitors of DdlB that could include both, an ATP-competitive and D-Ala competitive moiety.
authors.affiliation: Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia.
authors.forename: Veronika
authors.initials: V
authors.lastname: Škedelj
authors.forename: Emilija
authors.initials: E
authors.lastname: Arsovska
authors.forename: Tihomir
authors.initials: T
authors.lastname: Tomašić
authors.forename: Ana
authors.initials: A
authors.lastname: Kroflič
authors.forename: Vesna
authors.initials: V
authors.lastname: Hodnik
authors.forename: Martina
authors.initials: M
authors.lastname: Hrast
authors.forename: Marija
authors.initials: M
authors.lastname: Bešter-Rogač
authors.forename: Gregor
authors.initials: G
authors.lastname: Anderluh
authors.forename: Stanislav
authors.initials: S
authors.lastname: Gobec
authors.forename: Julieanne
authors.initials: J
authors.lastname: Bostock
authors.forename: Ian
authors.initials: I
authors.lastname: Chopra
authors.forename: Alex J
authors.initials: AJ
authors.lastname: O'Neill
authors.forename: Christopher
authors.initials: C
authors.lastname: Randall
authors.forename: Anamarija
authors.initials: A
authors.lastname: Zega
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D004926:Escherichia coli / Q000187:drug effects* / Q000201:enzymology*; D020128:Inhibitory Concentration 50; D008826:Microbial Sensitivity Tests; D062105:Molecular Docking Simulation; D010453:Peptide Synthases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D011743:Pyrimidines / Q000737:chemistry / Q000494:pharmacology*; D013816:Thermodynamics
chemical_list: D000900:Anti-Bacterial Agents; D004791:Enzyme Inhibitors; D011743:Pyrimidines; D000255:Adenosine Triphosphate; D010453:Peptide Synthases; C019638:D-alanylalanine synthetase