References
- Loewen K, Schreiber Y, Kirlew M, et al. Community-associated methicillin-resistant Staphylococcus aureus infection. Can Fam Physician. 2017;63(7):512–520.
- Boucher HW, Corey GR. Epidemiology of methicillin-resistant Staphylococcus aureus. Clin Infect Dis. 2008;46(S5):S344–S349.
- Macmorran E, Harch S, Athan E, et al. The rise of methicillin resistant Staphylococcus aureus: now the dominant cause of skin and soft tissue infection in Central Australia. Epidemiol Infect. 2017;145(13):2817–2826.
- Bugg TDH, Braddick D, Dowson CG, et al. Bacterial cell wall assembly: still an attractive antibacterial target. Trends Biotechnol. 2011;29(4):167–173.
- Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol. 2011;31(4):295–336.
- Barreteau H, Kova A, Boniface A, et al. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev. 2008;32(2):168–207.
- El Zoeiby A, Sanschagrin F, Levesque RC. Structure and function of the Mur enzymes: development of novel inhibitors. Mol Microbiol. 2003;47(1):1–12.
- Smith CA. Structure, function and dynamics in the Mur family of bacterial cell wall ligases. J Mol Biol. 2006;362(4):640–655.
- Gordon E, Flouret B, Chantalat L, et al. Crystal Structure of UDP-N-acetylmuramoyl-l-alanyl-d-glutamate:meso-Diaminopimelate ligase from Escherichia coli. J Biol Chem. 2001;276(14):10999–11006.
- Ikeda M, Wachi M, Jung HK, et al. Homology among MurC, MurD, MurE and MurF proteins in Escherichia coli and that between Escherichia coli MurG and a possible MurG protein in Bacillus subtilis. J Gen Appl Microbiol. 1990;36(3):179–187.
- Bouhss A, Dementin S, Parquet C, et al. Role of the ortholog and paralog amino acid invariants in the active site of the UDP-MurNAc-L-alanine:D-glutamate ligase (MurD). Biochemistry. 1999;38(38):12240–12247.
- El-Sherbeini M, Geissler WM, Pittman J, et al. Cloning and expression of Staphylococcus aureus and Treptococcus pyogenes murD genes encoding uridine diphosphate N-acetylmuramoyl-L-alanine: D-glutamate ligases. Gene. 1998;210(1):117–125.
- Bertrand JA, Auger G, Fanchon E, et al. Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. EMBO J. 1997;16(12):3416–3425.
- Perdih A, Kotnik M, Hodoscek M, et al. Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD. Proteins. 2007;68(1):243–254.
- Walsh AW, Falk PJ, Thanassi J, et al. Comparison of the D-glutamate-adding enzymes from selected gram-positive and gram-negative bacteria. J Bacteriol. 1999;181(17):5395–5401.
- Gegnas LD, Waddell ST, Chabin RM, et al. Inhibitors of the bacterial cell wall biosynthesis enzyme MurD. Bioorg Med Chem Lett. 1998;8(13):1643–1648.
- Gobec S, Urleb U, Auger G, et al. Synthesis and biochemical evaluation of some novel N-acyl phosphono- and phosphinoalanine derivatives as potential inhibitors of the D-glutamic acid-adding enzyme. Die Pharmazie. 2001;56(4):295–297.
- Strancar K, Blanot D, Gobec S. Design, synthesis and structure–activity relationships of new phosphinate inhibitors of MurD. Bioorg Med Chem Lett. 2006;16:343–348.
- Auger G, van Heijenoort J, Blanot D, et al. Synthesis of N-Acetylmuramic acid derivatives as potential inhibitors of the D-glutamic acid-adding enzyme. J Prakt Chem. 1995;337(1):351–357.
- Sova M, Kovac A, Turk S, et al. Phosphorylated hydroxyethylamines as novel inhibitors of the bacterial cell wall biosynthesis enzymes MurC to MurF. Bioorg Chem. 2009;37(6):217–222.
- Pratviel-Sosa F, Acher F, Trigalo F, et al. Effect of various analogues of D-glutamic acid on the D-glutamate-adding enzyme from Escherichia coli. FEMS Microbiol Lett. 1994;115:223–228.
- Kotnik M, Humljan J, Contreras-Martel C, et al. Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase. J Mol Biol. 2007;370(1):107–115.
- Humljan J, Kotnik M, Contreras-Martel C, et al. Novel naphthalene-N-sulfonyl-D-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme. J Med Chem. 2008;51(23):7486–7494.
- Perdih A, Bren U, Solmajer T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase. J Mol Model. 2009;15(8):983–996.
- Zidar N, TomašIć T, ŠInk R, et al. Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine-2,4-dione inhibitors of MurD ligase. J Med Chem. 2010;53(18):6584–6594.
- Zidar N, Tomasic T, Sink R, et al. New 5-benzylidenethiazolidin-4-one inhibitors of bacterial MurD ligase: design, synthesis, crystal structures, and biological evaluation. Eur J Med Chem. 2011;46(11):5512–5523.
- Sosic I, Barreteau H, Simcic M, et al. Second-generation sulfonamide inhibitors of D-glutamic acid-adding enzyme: activity optimisation with conformationally rigid analogues of D-glutamic acid. Eur J Med Chem. 2011;46:2880–2894.
- Perdih A, Wolber G, Solmajer T. Molecular dynamics simulation and linear interaction energy study of D-Glu-based inhibitors of the MurD ligase. J Comput Aided Mol Des. 2013;27(8):723–738.
- Perdih A, Hrast M, Barreteau H, et al. Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF). Bioorg Med Chem. 2014;22(15):4124–4134.
- Tomasc T, Sink R, Zidar N, et al. Dual inhibitor of MurD and MurE ligases from Escherichia coli and Staphylococcus aureus. ACS Med Chem Lett. 2012;3:626–630.
- Turk S, Kovac A, Boniface A, et al. Discovery of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurF by structure-based virtual screening. Bioorg Med Chem. 2009;17(5):1884–1889.
- Simcic M, Pureber K, Kristan K, et al. A novel 2-oxoindolinylidene inhibitor of bacterial MurD ligase: enzyme kinetics, protein-inhibitor binding by NMR and a molecular dynamics study. Eur J Med Chem. 2014;83:92–101.
- Azam MA, Jupudi S, Saha N, et al. Combining molecular docking and molecular dynamics studies for modelling Staphylococcus aureus MurD inhibitory activity. SAR QSAR Environ Res. 2019;30(1):1–20.
- Azam MA, Jupudi S. Structure based virtual screening to identify inhibitors against Staphylococcus aureus MurD Enzyme. Stru Chem. 2019;1–11. DOI: 10.1007/s11224-019-01330-z
- Mahran MA, William S, Ramzy F, et al. Synthesis and in vitro evaluation of new benzothiazole berivatives as schistosomicidal agents. Molecules. 2007;12(3):622–633.
- Holsworth D, Waaler J, Machon O, et al. Azole derivatives as WTN pathway inhibitors. US Pat. 2012/US 8,883,827 A1, Aug. 16, Appl. No.: 13/376,202. PCT Filed: Jun. 7, 2010.
- Clinical and Laboratory Standard Institute (CLSI). Methods for dilution antibacterial susceptibility test for bacteria that grow aerobically, 7th ed. Approved Standard (MA7-A7); Clinical and Laboratory Standard Institute: Wayne. 2007. 27:133.
- Auger G, Martin L, Bertrand J, et al. Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli. Prot Express Purif. 1998;13(1):23–29.
- Lanzetta PA, Alvarez LJ, Reinach PS, et al. An improved assay for nanomole amounts of inorganic phosphate. Anal Biochem. 1979;100(1):95–97.
- Sastry MG, Adzhigirey M, Day T, et al. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des. 2013;27:221–234.
- Jacobson MP, Pincus DL, Rapp CS, et al. A hierarchical approach to all-atom protein loop prediction. Proteins. 2004;55(2):351–367.
- Li J, Abel R, Zhu K, et al. The VSGB 2.0 Model: a next generation energy model for high resolution protein structure modelling. Proteins. 2011;79(10):2794–2812.
- Harder E, Damm W, Maple J, et al. OPLS3: A force field providing broad coverage of drug-like small molecules and protein. J Chem Theory Comput. 2016;12(1):281–296.
- Jorgensen WL, Madura JD. Temperature and size dependence for Monte Carlo simulations of TIP4P water. Mol Phys. 1985;56(6):1381–1392.
- Lawrence CP, Skinner JL. Flexible TIP4P model for molecular dynamics simulation of liquid water. Chem Phys Lett. 2003;372(5-6):842–847.
- Essmann U, Perera L, Berkowit ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995;103(19):8577–8593.
- Martyna GJ, Klein ML, Tuckerman M. Nose-Hoover chains: the canonical ensemble via continuous dynamics. J Chem Phys. 1992;97(4):2635–2643.
- Martyna GJ, Tobias DJ, Klein ML. Constant-pressure molecular dynamics algorithms. J Chem Phys. 1994;101(5):4177–4189.