Novel 2-thioxothiazolidin-4-one inhibitors of bacterial MurD ligase targeting d-Glu- and diphosphate-binding sites

European Journal of Medicinal Chemistry

Volumn 46, Issue 9, 2011, Pages 3964-3975

  Tomašić, Tihomir ^a   Kovač, Andreja ^a   Simčič, Mihael ^b   Blanot, Didier ^c   Grdadolnik, Simona Golič ^b,d   Gobec, Stanislav ^a   Kikelj, Danijel ^a   Peterlin Mašič, Lucija ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^c INSTITUTE FOR INTEGRATIVE BIOLOGY OF THE CELL I2BC   (France)

^d EN FIST CENTRE OF EXCELLENCE   (Slovenia)

Author keywords

2 Thioxothiazolidin 4 one; Antibacterial agent; Glutamic acid; Inhibitor; Mur ligase; Protein NMR

Indexed keywords

2 (3 ((4 OXO 2 THIOXOTHIAZOLIDIN 5 YLIDENE)METHYL)BENZAMIDO)PENTANEDIOIC ACID; 2 (4 ((4 OXO 2 THIOXOTHIAZOLIDIN 5 YLIDENE)METHYL)BENZAMIDO)PENTANEDIOIC ACID; 2 IMINOTHIAZOLIDIN 4 ONE; 2 THIOXOTHIAZOLIDIN 4 ONE; 2 THIOXOTHIAZOLIDIN 4 ONE INHIBITOR; 2,4 THIAZOLIDINEDIONE DERIVATIVE; ANTIINFECTIVE AGENT; BENZYLIDENE DERIVATIVE; GLUTAMIC ACID; GLUTATHIONE; HYDANTOIN DERIVATIVE; LIGASE; PYROPHOSPHATE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; DRUG BINDING; DRUG SYNTHESIS; ESCHERICHIA COLI; IC 50; NONHUMAN; NUCLEAR MAGNETIC RESONANCE;

BINDING SITES; CATALYTIC DOMAIN; ENZYME INHIBITORS; ESCHERICHIA COLI; INHIBITORY CONCENTRATION 50; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE SYNTHASES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROPHOTOMETRY, INFRARED; THIAZOLIDINES;

EID: 80052925406     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2011.05.070     Document Type: Article

References (49)

1. D.M. Livermore Bacterial resistance: origins, epidemiology, and impact Clin. Infect. Dis. 36 2003 11 23
2. I. Chopra, C. Schofield, M. Everett, A. O'Neill, K. Miller, M. Wilcox, J.M. Frre, M. Dawson, L. Czaplewski, U. Urleb, and P. Courvalin Treatment of health-care-associated infections caused by Gram-negative bacteria: a consensus statement Lancet Infect. Dis. 8 2008 133 139
3. L.B. Rice Unmet medical needs in antibacterial therapy Biochem. Pharmacol. 71 2006 991 995
4. P. Nordmann, T. Naas, N. Fortineau, and L. Poirel Superbugs in the coming new decade; multidrug resistance and prospects for treatment of Staphylococcus aureus, Enterococcus spp. and Pseudomonas aeruginosa in 2010 Curr. Opin. Microbiol. 10 2007 436 440
5. W. Vollmer, D. Blanot, and M.A. de Pedro Peptidoglycan structure and architecture FEMS Microbiol. Rev. 32 2008 149 167
6. H. Barreteau, A. Kovač, A. Boniface, M. Sova, S. Gobec, and D. Blanot Cytoplasmic steps of peptidoglycan biosynthesis FEMS Microbiol. Rev. 32 2008 168 207
7. A. El Zoeiby, F. Sanschagrin, and R.C. Levesque Structure and function of the Mur enzymes: development of novel inhibitors Mol. Microbiol. 47 2003 1 12
8. J.A. Bertrand, G. Auger, L. Martin, E. Fanchon, D. Blanot, D. Le Beller, J. van Heijenoort, and O. Dideberg Determination of the MurD mechanism through crystallographic analysis of enzyme complexes J. Mol. Biol. 289 1999 579 590
9. A. Bouhss, S. Dementin, J. van Heijenoort, C. Parquet, and D. Blanot MurC and MurD synthetases of peptidoglycan biosynthesis: borohydride trapping of acyl-phosphate intermediates Methods Enzymol. 354 2002 189 196
10. J.J. Emanuele, H.Y. Jin, J. Yanchunas, and J.J. Villafranca Evaluation of the kinetic mechanism of Escherichia coli uridine diphosphate-N-acetylmuramate: l-alanine ligase Biochemistry 36 1997 7264 7271
11. M.S. Anderson, S.S. Eveland, H.R. Onishi, and D.L. Pompliano Kinetic mechanism of the Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme: use of a glutathione S-transferase fusion Biochemistry 35 1996 16264 16269
12. C.A. Smith Structure, function and dynamics in the mur family of bacterial cell wall ligases J. Mol. Biol. 362 2006 640 655
13. M.E. Tanner, S. Vaganay, J. van Heijenoort, and D. Blanot Phosphinate inhibitors of the d-glutamic acid-adding enzyme of peptidoglycan biosynthesis J. Org. Chem. 61 1996 1756 1760
14. K. Štrancar, D. Blanot, and S. Gobec Design, synthesis and structure-activity relationships of new phosphinate inhibitors of MurD Bioorg. Med. Chem. Lett. 16 2006 343 348
15. M. Kotnik, J. Humljan, C. Contreras-Martel, M. Oblak, K. Kristan, M. Hervé, D. Blanot, U. Urleb, S. Gobec, A. Dessen, and T. Šolmajer Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase J. Mol. Biol. 370 2007 107 115
16. J. Humljan, M. Kotnik, C. Contreras-Martel, D. Blanot, U. Urleb, A. Dessen, T. Šolmajer, and S. Gobec Novel naphthalene-N-sulfonyl-d-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme J. Med. Chem. 51 2008 7486 7494
17. A. Perdih, A. Kovač, G. Wolber, D. Blanot, S. Gobec, and T. Šolmajer Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach Bioorg. Med. Chem. Lett. 19 2009 2668 2673
18. S. Turk, A. Kovač, A. Boniface, J.M. Bostock, I. Chopra, D. Blanot, and S. Gobec Discovery of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes MurD and MurF by structure-based virtual screening Bioorg. Med. Chem. 17 2009 1884 1889
19. J.R. Horton, J.M. Bostock, I. Chopra, L. Hesse, S.E. Phillips, D.J. Adams, A.P. Johnson, and C.W. Fishwick Macrocyclic inhibitors of the bacterial cell wall biosynthesis enzyme MurD Bioorg. Med. Chem. Lett. 13 2003 1557 1560
20. C. Paradis-Bleau, M. Beaumont, L. Boudreault, A. Lloyd, F. Sanschagrin, T.D. Bugg, and R.C. Levesque Selection of peptide inhibitors against the Pseudomonas aeruginosa MurD cell wall enzyme Peptides 27 2006 1693 1700
21. K. Kristan, M. Kotnik, M. Oblak, and U. Urleb New high-throughput fluorimetric assay for discovering inhibitors of UDP-N-acetylmuramyl-l-alanine: d-glutamate (MurD) ligase J. Biomol. Screen. 14 2009 412 418
22. M. Kotnik, P. Štefanič Anderluh, and A. Preželj Development of novel inhibitors targeting intracellular steps of peptidoglycan biosynthesis Curr. Pharm. Design 13 2007 2283 2309
23. T. Tomašić, N. Zidar, V. Rupnik, A. Kovač, D. Blanot, S. Gobec, D. Kikelj, and L. Peterlin Maši&ccaron Synthesis and biological evaluation of new glutamic acid-based inhibitors of MurD ligase Bioorg. Med. Chem. Lett. 19 2009 153 157
24. Gold V4.1 is available from The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK, www.ccdc.cam.ac.uk.
25. C.S. Rye, and J.B. Baell Phosphate isosteres in medicinal chemistry Curr. Med. Chem. 12 2005 3127 3141
26. N. Zidar, T. Tomašić, R. Šink, V. Rupnik, A. Kovač, S. Turk, D. Patin, D. Blanot, C. Contreras Martel, A. Dessen, M. Müller Premru, A. Zega, S. Gobec, L. Peterlin Mašič, and D. Kikelj Discovery of novel 5-benzylidenerhodanine and 5-benzylidenethiazolidine- 2,4-dione inhibitors of MurD ligase J. Med. Chem. 53 2010 6584 6594
27. T. Tomašić, N. Zidar, A. Kovač, S. Turk, M. Simčič, D. Blanot, M. Müller-Premru, M. Filipič, S.G. Grdadolnik, A. Zega, M. Anderluh, S. Gobec, D. Kikelj, and L. Peterlin Mašič 5-Benzylidenethiazolidin-4-ones as multitarget inhibitors of bacterial Mur ligases ChemMedChem 5 2010 286 295
28. J.B. Baell, and G.A. Holloway New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays J. Med. Chem. 53 2010 2719 2740
29. R. Šink, S. Gobec, S. Pečar, and A. Zega False positives in the early stages of drug discovery Curr. Med. Chem. 17 2010 4231 4255
30. T. Ishida, Y. In, M. Inoue, Y. Ueno, C. Tanaka, and N. Hamanaka Structural elucidation of epalrestat(Ono-2235), a potent aldose reductase inhibitor, and isomerization of its double-bonds Tetrahedron Lett. 30 1989 959 962
31. N. Zidar, J. Kladnik, and D. Kikelj A convenient synthesis of 4-benzyl-2-(2-(4-oxo-2-thioxothiazolidin-5-ylidene)ethyl)-2H-1, 4-benzoxazin-3(4H)-ones and 5-(2-(4-benzyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin- 2-yl)ethylidene)thiazolidine-2,4-diones Acta Chim. Slov 56 2009 635 642
32. K. Nakamura, M. Fujii, A. Ohno, and S. Oka NAD(P)+-NAD(P)H model. 52. Reduction of olefins by Hantzsch ester on silica gel Tetrahedron Lett. 25 1984 3983 3986
33. P.A. Lanzetta, L.J. Alvarez, P.S. Reinach, and O.A. Candia Improved assay for nanomole amounts of inorganic-phosphate Anal. Biochem. 100 1979 95 97
34. S.L. McGovern, B.T. Helfand, B. Feng, and B.K. Shoichet A specific mechanism of nonspecific inhibition J. Med. Chem. 46 2003 4265 4272
35. E.B. Grant, D. Guiadeen, E.Z. Baum, B.D. Foleno, H. Jin, D.A. Montenegro, E.A. Nelson, K. Bush, and D.J. Hlasta The synthesis and SAR of rhodanines as novel class C β-lactamase inhibitors Bioorg. Med. Chem. Lett. 10 2000 2179 2182
36. T. Tomašić, and L. Peterlin Maši&ccaron Rhodanine as a privileged scaffold in drug discovery Curr. Med. Chem. 16 2009 1596 1629
37. 13C-labeled methyl groups J. Am. Chem. Soc. 122 2000 7898 7904
38. M. Simčič, M. Hodošček, J. Humljan, K. Kristan, U. Urleb, D. Kocjan, and S. Golič Grdadolnik NMR and molecular dynamics study of the binding mode of naphthalene-N-sulfonyl-d-glutamic acid derivatives: novel MurD ligase inhibitors J. Med. Chem. 52 2009 2899 2908
39. L. Kay, P. Keifer, and T. Saarinen Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity J. Am. Chem. Soc. 114 1992 10663 10665
40. T.D. Goddard, D.G. Kneller, SPARKY 3, University of California, San Francisco (USA) (source: http://www.cgl.ucsf.edu/home/sparky/).
41. F.H. Schumann, H. Riepl, T. Maurer, W. Gronwald, K.P. Neidig, and H.R. Kalbitzer Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions J. Biomol. NMR 39 2007 275 289
42. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
43. A.D. MacKerell, D. Bashford, M. Bellott, R.L. Dunbrack, J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B. 102 1998 3586 3616
44. A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
45. K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, and A.D. Mackerell Jr. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields J. Comput. Chem. 31 2010 671 690
46. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33-8, 27-8
47. T.A. Halgren Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94 J. Comput. Chem. 17 1996 490 519
48. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 267 1997 727 748
49. Pymol is available from Delano Scientific LLC, San Francisco, CA, http://pymol.sourceforge.net.