Background and Target Validation
Background: Mur ligases as targets for new antibiotics (DOI)
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MurC ligase or UDP-N-acetylmuramoyl-L-alanine ligase adds L-alanine (L-Ala) to the UDP precursor---UDP-MurNAc (UNAM) and generates UDP-N-acetylmuramoyl-L-alanine (UMA).
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MurD ligase or UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase catalyzes the conversion of UMA, D-glutamate (D-Glu) and ATP to UDP-N-acetylmuramoyl-L-alanine-D-glutamate and ADP, giving UDP-MurNAc-L-Ala-D-Glu (UMAG).
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MurE ligase or UDP-N-acetylmuramoyl-L-alaninyl-D-glutamate-2,6-diaminopimelate ligase adds meso-diaminpimelate (mA2pm) to UMAG and forms UDP-MurNAc-L-Ala-D-Glu-mA2pm, also known as UDP-N-acetylmuramoyl:tripeptide (UMT).
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MurF ligase or UDP-N-acetylmuramoyl-L-alanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase adds D-alanyl-D-alanine (D-Ala-D-Ala) to peptidoglycan stems and achieves UDP-MurNAc-L-Ala-D-Glu-mA2pm/L-Lys-D-Ala-D-Ala, also known as UDP-N-acetylmuramoyl:pentapeptide (UMPP).
The enzyme mechanism has been studied (DOI) and multiple crystal structures published. The image below shows PDB code 3uag highlighting the position of ADP (coloured blue) and UDP-N-acetylmuramoyl-L-alanine (UMA coloured green) for MurD Escherichia coli (strain K12).
You can view and rotate the 3D structure of the enzyme here. All four enzymes are topologically similar.
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There is a recent review of known inhibitors Mur Ligase Inhibitors as Anti-bacterials: A Comprehensive Review and another from Gobec et al in 2014.
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Novel pyrazolopyrimidine-based inhibitors of Pseudomonas aeruginosa MurC have been reported CHEMBL3355659 derived from a high-throughput screening hit DOI.
Radio-labeled precursor incorporation showed these compounds selectively inhibited peptidoglycan biosynthesis, and genetic studies confirmed the target of pyrazolopyrimidines to be MurC. CHEMBL3355659 was a potent enzyme inhibitor (IC50 0.001 uM), but showed poor activity against wild-type bacteria. However, it showed appreciable antibacterial activity against efflux-deficient mutants, strongly suggesting the low antibacterial potency arose from an efflux problem (also examined in a separate publication (DOI).
- A series of phosphorylated hydroxyethylamines have been evaluated for inhibitory activity against Mur ligases. The most potent inhibitor CHEMBL473552 had an IC50 of 6 μM on MurE.
- A series of hydroxy-substituted 5-benzylethazolidine-4- compounds were synthesized and tested as inhibitors of Mur ligase. (DOI) CHEMBL2170127 has the strongest inhibitory activity on MurD-F, with an IC50 value between 2 and 6 μm.
- A virtual screening campaign combining three-dimensional structure-based pharmacophores and molecular docking calculations (DOI) identified benzene 1,3-dicarboxylic acid derivatives shown to possess dual MurD and MurE inhibitory activity, CHEMBL562422 and CHEMBL564223.
This work has been continued (DOI) to improve activity against all Escherichia coli MurC–MurF enzymes to afford CHEMBL3310464. Steady-state kinetics studies suggested this class to act as competitive inhibitors of the MurD enzyme towards d-Glu.
Steady-state kinetics studies from sequential work (DOI) suggested CHEMBL564223 acts as an ATP competitive inhibitor against MurD enzyme. Furan-based benzene mono- and dicarboxylic acid derivatives, like PubChem2287101 possessed promising multiply inhibition activity against S. aureus Mur ligases.
- Dual inhibitors of MurD and MurE Ligases have been reported DOI with activities against Escherichia coli and Staphylococcus aureus (IC50 values between 6.4 and 180 μM). An example being CHEMBL2151317.
- The activities of known inhibitors of Escherichia coli MurD have been evaluated against the MurD enzymes from Staphylococcus aureus, Streptococcus pneumoniae, Borrelia burgdorferi and Mycobacterium tuberculosis (DOI). Many of the E. coli MurD inhibitors were less potent against the other four species. Examination of the sequences suggests that Leu416 in E. Coli but Phe or Trp in other species may be responsible for the differences in activity observed.
- Two small molecule inhibitors of Streptococcus pneumonia MurF have been identified by NMR screening (DOI) CHEMBL327236 and CHEMBL329363.
The X-ray structures were subsequently determined 2AM1 and 2AM2. The uridine–ribose binding site overlaps with the corresponding ligand binding site observed for these two compounds.
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In general the majority of MurD inhibitors reported to date fail to show robust antibacterial activity, with poor cell penetration thought to be a common issue.
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For many of these inhibitors the crystal structures have been determined, and a selection are shown overlaid below (inhibitors coloured magenta). These inhibitors occupy the UMA binding site.
