Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF)

Bioorganic and Medicinal Chemistry

Volumn 22, Issue 15, 2014, Pages 4124-4134

  Perdih, Andrej ^a,b   Hrast, Martina ^c   Barreteau, Hélène ^d   Gobec, Stanislav ^c   Wolber, Gerhard ^b   Solmajer, Tom ^a  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF LJUBLJANA   (Slovenia)

^d UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Antibacterial agents; Bacterial Mur (MurC MurF) ligase; Drug design; Linear Interaction Energy (LIE) method; Molecular docking; Molecular dynamics (MD); Structure based pharmacophores; Virtual screening

Indexed keywords

BENZENE 1,3 DICARBOXYLIC ACID 2,5 DIMETHYLPYRROLE DERIVATIVE; LIGASE; MURC LIGASE; MURD LIGASE; MURE LIGASE; MURF LIGASE; PYRROLE DERIVATIVE; UNCLASSIFIED DRUG; 2,5-DIMETHYLPYRROLE; ENZYME INHIBITOR; ESCHERICHIA COLI PROTEIN; PEPTIDE SYNTHASE; PROTEIN BINDING; UDP-N-ACETYLMURAMOYLALANINE-D-GLUTAMATE LIGASE;

ARTICLE; BINDING SITE; DRUG ANALYSIS; DRUG DESIGN; DRUG STRUCTURE; ENERGY TRANSFER; ENZYME BINDING; ENZYME INHIBITION; ENZYME KINETICS; ESCHERICHIA COLI; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; PHARMACOPHORE; STEADY STATE; ANTAGONISTS AND INHIBITORS; CHEMISTRY; ENZYMOLOGY; KINETICS; METABOLISM; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION;

BINDING SITES; ENZYME INHIBITORS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; MOLECULAR DYNAMICS SIMULATION; PEPTIDE SYNTHASES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PYRROLES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84905086241     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2014.05.058     Document Type: Article

References (44)

1. L.L. Silver Biochem. Pharmacol. 71 2006 996
2. E.D. Brown, and G.D. Wright Chem. Rev. 105 2005 759
3. L.L. Silver Clin. Microbiol. Rev. 24 2011 71
4. W. Vollmer, D. Blanot, and M.A. de Pedro FEMS Microbiol. Rev. 32 2008 149
5. H. Barreteau, A. Kovač, A. Boniface, M. Sova, S. Gobec, and D. Blanot FEMS Microbiol. Rev. 32 2008 168
6. R. Šink, H. Barreteau, D. Patin, D. Mengin-Lecreulx, S. Gobec, and D. Blanot Biomol. Concepts 4 2013 539
7. J. van Heijenoort Nat. Prod. Rep. 18 2001 503
8. C.S. Smith J. Mol. Biol. 362 2006 640
9. J.A. Bertrand, E. Fanchon, L. Martin, L. Chantalat, G. Auger, D. Blanot, J. van Heijenoort, and O. Dideberg J. Mol. Biol. 301 2000 1257
10. A. Perdih, M. Kotnik, M. Hodoscek, and T. Solmajer Proteins: Struct., Funct. Bioinf. 68 2007 243
11. A. Perdih, and T. Solmajer Comput. Theor. Chem. 979 2012 73
12. A. Perdih, M. Hrast, H. Barreteau, S. Gobec, G. Wolber, and T. Solmajer J. Chem. Inf. Model. 54 2014 1451
13. J.A. Bertrand, G. Auger, L. Martin, E. Fanchon, D. Blanot, D. Le Beller, J. van Heijenoort, and O. Dideberg J. Mol. Biol. 289 1999 579
14. M.S. Anderson, S.S. Eveland, H. Onishi, and D.L. Pompliano Biochemistry 35 1996 16264
15. J.J. Emanuele Jr., H. Jin, J. Yanchunas Jr., and J.J. Villafranca Biochemistry 36 1997 7264
16. A. Perdih, M. Hodoscek, and T. Solmajer Proteins: Struct., Funct. Bioinf. 74 2009 744
17. A. Bouhss, S. Dementin, J. van Heijenoort, C. Parquet, and D. Blanot Methods Enzymol. 354 2002 189
18. P.J. Falk, K.M. Ervin, K.S. Volk, and H.-T. Ho Biochemistry 35 1996 1417
19. A.E. Zoeiby, F. Sanschagrin, and R.C. Levesque Mol. Microbiol. 47 2002 1
20. M.E. Tanner, S. Vaganay, J. van Heijenoort, and D. Blanot J. Org. Chem. 61 1996 1756
21. M. Kotnik, J. Humljan, C. Contreras-Martel, M. Oblak, K. Kristan, M. Hervé, D. Blanot, U. Urleb, S. Gobec, A. Dessen, and T. Solmajer J. Mol. Biol. 370 2007 107
22. J. Humljan, M. Kotnik, C. Contreras-Martel, D. Blanot, U. Urleb, A. Desssen, T. Solmajer, and S. Gobec J. Med. Chem. 51 2008 7486
23. A. Perdih, U. Bren, and T. Solmajer J. Mol. Model. 15 2009 983
24. A. Perdih, G. Wolber, and T. Solmajer J. Comput.-Aided Mol. Des. 27 2013 723
25. A. Perdih, A. Kovač, G. Wolber, D. Blanot, S. Gobec, and T. Solmajer Bioorg. Med. Chem. Lett. 19 2009 2668
26. I. Sosič, H. Barreteau, M. Simčič, R. Šink, J. Cesar, A. Zega, S.G. Grdadolnik, C. Contreras-Martel, A. Dessen, A. Amoroso, B. Joris, D. Blanot, and S. Gobec Eur. J. Med. Chem. 46 2011 2880
27. T. Tomašić, R. Šink, N. Zidar, A. Fic, C. Contreras-Martel, A. Dessen, D. Patin, D. Blanot, M. Premru-Mullerm, S. Gobec, A. Zega, D. Kikelj, and L. Peterlin Mašič ACS Med. Chem. Lett. 3 2012 626
28. T. Tomašić, N. Zidar, A. Kovač, S. Turk, M. Simčič, D. Blanot, M. Premru-Mullerm, M. Filipič, S. Golič Grdadolnik, A. Zega, M. Anderluh, S. Gobec, D. Kikelj, and L. Peterlin Mašič ChemMedChem 5 2010 286
29. S.L. McGovern, and B.K. Stoichet J. Med. Chem. 46 2003 1478
30. Catalyst; Accelrys Software: San Diego.
31. G. Wolber, and T. Langer J. Chem. Inf. Model. 45 2005 160
32. G. Wolber, A. Dornhofer, and T. Langer J. Comput.-Aided Mol. Des. 20 2006 773
33. A. Cereto-Massague, L. Guasch, C. Valls, M. Mulero, G. Pujadas, and S. Garcia-Vallve Bioinformatics 28 2012 1662
34. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor J. Mol. Biol. 267 1997 727
35. E. Gordon, B. Flouret, L. Chantalat, J. van Heijenoort, D. Mengin-Lecreulx, and O. Dideberg J. Biol. Chem. 276 2001 10999
36. J. Åqvist, C. Medina, and J.E. Samuelson Protein Eng. 7 1994 385
37. J. Marelius, K. Kolmodin, I. Feierberg, and J. Åqvist J. Mol. Graph. Model. 16 1998 213
38. P.A. Bash, L.L. Ho, A.D. MacKerell, D. Levine, and P. Hallstrom Proc. Natl. Acad. Sci. U.S.A. 93 1996 3698
39. C.-G. Wermuth The Practice of Medicinal Chemistry 3r d ed. 2008 Academic Press
40. OMEGA 2.4.6; OpenEye Scientific Software Inc: Santa Fe, NM, 2012.
41. P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson, and M.T. Stahl J. Chem. Inf. Model. 50 2010 572
42. J. Kirchmair, P. Markt, S. Distinto, G. Wolber, and T. Langer J. Comput. Aided Mol. Des. 22 2008 213
43. G. Auger, L. Martin, J. Bertrand, P. Ferrari, E. Fanchon, S. Vaganay, Y. Petillot, J. van Heijenoort, D. Blanot, and O. Dideberg Protein Expression Purif. 13 1998 23
44. P.A. Lanzetta, L.J. Alvarez, P.S. Reinach, and O. Candia Anal. Biochem. 100 1979 95