Design, synthesis and evaluation of second generation MurF inhibitors based on a cyanothiophene scaffold

European Journal of Medicinal Chemistry

Volumn 73, Issue , 2014, Pages 83-96

  Hrast, Martina ^a   Anderluh, Marko ^a   Knez, Damijan ^a   Randall, Christopher P ^b   Barreteau, Hélène ^c   O'Neill, Alex J ^b   Blanot, Didier ^c   Gobec, Stanislav ^a  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

Antibacterials; Enzyme inhibitors; MurF; Peptidoglycan

Indexed keywords

2 (3 CARBOXY 4 CHLOROPHENOXY)ETHAN AMMONIUM TRIFLUOROACETATE; 2 [2 CHLORO 5 [2 (2,2,2-TRIFLUOROACETAMIDO)ETHOXY] BENZAMIDO] 3 CYANO 4,5,6,7 TETRA HYDROTHIENO [2,3 C]PYRIDIN 6 IUM TRIFLUOROACETATE; 2 CHLORO 5 [2 (2,2,2 TRIFLUOROACETAMIDO)ETHOXY]BENZOIC ACID; 3 (2 AMINOETHOXY) N (3 CYANO 4,5,6,7 TETRAHYDROBENZO[B] THIOPHEN 2 YL)BENZAMIDE; 3 [(3 CYANO 4,5,6,7 TETRAHYDROBENZO[B]THIOPHEN 2 YL)CARBAMOYL]PHENYL ACETATE; 3 ACETOXYBENZOIC ACID; 5 [(2 AMINOETHYL)SULFAMOYL] 2,4 DICHLORO N (3 CYANO 4,5,6,7 TETRAHYDRO 1BENZOTHIOPHEN 2 YL)BENZAMIDE HYDROCHLORIDE; 5 [2 (TERT BUTOXYCARBONYLAMINO)ETHOXY) 2 CHLOROBENZOIC ACID; 5 [2 (TERT BUTOXYCARBONYLAMINO)ETHOXY] 2 CHLOROBENZOIC ACID; 5 [N [2 [(TERT BUTOXYCARBONYL)AMINO]ETHYL]SULFAMOYL] 2,4 DICHLOROBENZOIC ACID; ANTIBIOTIC AGENT; LIGASE INHIBITOR; METHYL 2 CHLORO 5 HYDROXYBENZOATE; METHYL 5 [2 [(TERT BUTOXYCARBONYL)AMINO]ETHOXY] 2 CHLOROBENZOATE; MUSCLE RING FINGER 1 PROTEIN; N (3 CYANO 4,5,6,7 TETRAHYDROBENZO[B]THIOPHEN 2 YL) 3 (2 GUANIDINOETHOXY) BENZANAMIDE; N (3 CYANO 4,5,6,7 TETRAHYDROBENZO[B]THIOPHEN 2-YL) 3 HYDROXYBENZAMIDE; TERT BUTYL [2 [2,4 DICHLORO 5 [(3 CYANO 4,5,6,7 TETRAHYDROBENZO[B]THIOPHEN 2 YL)CARBAMOYL] PHENYLSULFONAMIDO]ETHYL CARBAMATE; THIOPHENE DERIVATIVE; UNCLASSIFIED DRUG;

ANTIBACTERIAL ACTIVITY; ARTICLE; BACTERIAL STRAIN; COMPETITIVE INHIBITION; DRUG DESIGN; DRUG SCREENING; DRUG STRUCTURE; DRUG SYNTHESIS; DRUG TARGETING; ESCHERICHIA COLI; NONHUMAN; STAPHYLOCOCCUS AUREUS;

ANTIBACTERIALS; ENZYME INHIBITORS; MURF; PEPTIDOGLYCAN;

ANTI-BACTERIAL AGENTS; DRUG DESIGN; ENZYME INHIBITORS; ESCHERICHIA COLI; MICROBIAL SENSITIVITY TESTS; MOLECULAR STRUCTURE; PEPTIDE SYNTHASES; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE; STRUCTURE-ACTIVITY RELATIONSHIP; THIOPHENES;

EID: 84891705572     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2013.11.031     Document Type: Article

References (35)

1. A.J. Alanis Resistance to antibiotics: are we in the post-antibiotic era? Arch. Med. Res. 36 2005 697 705 (Pubitemid 41436239)
2. P.C. Appelbaum 2012 and beyond: potential for the start of a second pre-antibiotic era? J. Antimicrob. Chemother. 67 2012 2062 2068
3. I. Chopra The 2012 Garrod Lecture: discovery of antibacterial drugs in the 21st century J. Antimicrob. Chemother. 68 2013 496 505
4. T.D.H. Bugg, D. Braddick, C.G. Dowson, and D.I. Roper Bacterial cell wall assembly: still an attractive antibacterial target Trends Biotechnol. 29 2011 167 173
5. A. Gautam, R. Vyas, and R. Tewari Peptidoglycan biosynthesis machinery: a rich source of drug targets Crit. Rev. Biotechnol. 31 2011 295 336
6. D.W. Green The bacterial cell wall as a source of antibacterial targets Expert Opin. Ther. Targets 6 2002 1 20
7. 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 (Pubitemid 351257820)
8. 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 (Pubitemid 36051319)
9. C.A. Smith Structure, function and dynamics in the mur family of bacterial cell wall ligases J. Mol. Biol. 362 2006 640 655 (Pubitemid 44332429)
10. D.J. Miller, S.M. Hammond, D. Anderluzzi, and T.D.H. Bugg Aminoalkylphosphinate inhibitors of d-Ala-d-Ala adding enzyme J. Chem. Soc. Perkin Trans. 1 1998 131 142 (Pubitemid 128757891)
11. Y.G. Gu, A.S. Florjancic, R.F. Clark, T. Zhang, C.S. Cooper, D.D. Anderson, C.G. Lerner, J.O. McCall, Y. Cai, C.L. Black-Schaefer, G.F. Stamper, P.J. Hajduk, and B.A. Beutel Structure-activity relationships of novel potent MurF inhibitors Bioorg. Med. Chem. Lett. 14 2004 267 270 (Pubitemid 38016215)
12. G.F. Stamper, K.L. Longenecker, E.H. Fry, C.G. Jakob, A.S. Florjancic, Y.G. Gu, D.D. Anderson, C.S. Cooper, T. Zhang, R.F. Clark, Y. Cia, C.L. Black-Schaefer, J. Owen McCall, C.G. Lerner, P.J. Hajduk, B.A. Beutel, and V.S. Stoll Structure-based optimization of MurF inhibitors Chem. Biol. Drug Des. 67 2006 58 65 (Pubitemid 43881387)
13. E.Z. Baum, S.M. Crespo-Carbone, D. Abbanat, B. Foleno, A. Maden, R. Goldschmidt, and K. Bush Utility of muropeptide ligase for identification of inhibitors of the cell wall biosynthesis enzyme MurF Antimicrob. Agents Chemother. 50 2006 230 236 (Pubitemid 43042926)
14. E.Z. Baum, S.M. Crespo-Carbone, A. Klinger, B.D. Foleno, I. Turchi, M. Macielag, and K. Bush A MurF inhibitor that disrupts cell wall biosynthesis in Escherichia coli Antimicrob. Agents Chemother. 51 2007 4420 4426 (Pubitemid 350209898)
15. E.Z. Baum, S.M. Crespo-Carbone, B.D. Foleno, L.D. Simon, J. Guillemont, M. Macielag, and K. Bush MurF inhibitors with antibacterial activity: effect on muropeptide levels Antimicrob. Agents Chemother. 53 2009 3240 3247
16. 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
17. S. Turk, M. Hrast, I. Sosič, H. Barreteau, D. Mengin-Lecreulx, D. Blanot, and S. Gobec Biochemical characterization of MurF from Streptococcus pneumoniae and the identification of a new MurF inhibitor through ligand-based virtual screening Acta Chim. Slov. 60 2013 294 299
18. M. Hrast, S. Turk, I. Sosič, D. Knez, C.P. Randall, H. Barreteau, C. Contreras-Martel, A. Dessen, A.J. O'Neill, D. Mengin-Lecreulx, D. Blanot, and S. Gobec Structure-activity relationships of new cyanothiophene inhibitors of the essential peptidoglycan biosynthesis enzyme MurF Eur. J. Med. Chem. 66 2013 32 45
19. P.D. Leeson, and A.M. Davis Time-related differences in the physical property profiles of oral drugs J. Med. Chem. 47 2004 6338 6348 (Pubitemid 39587257)
20. R. O'Shea, and H.E. Moser Physicochemical properties of antibacterial compounds: implication for drug discovery J. Med. Chem. 51 2008 2871 2878 (Pubitemid 351706014)
21. I. Dvoretzky, and G.H. Richter Formaldehyde condensation in the pyrazole series J. Org. Chem. 15 1950 1285 1288
22. P.A. Lanzetta, L.J. Alvarez, P.S. Reinach, and O.A. Candia An improved assay for nanomole amounts of inorganic phosphate Anal. Biochem. 100 1979 95 97 (Pubitemid 10157636)
23. 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 (Pubitemid 37153008)
24. J.K. Hobbs, K. Miller, and A.J. O'Neill et al. Consequences of daptomycin-mediated membrane damage in Staphylococcus aureus J. Antimicrob. Chemother. 62 2008 1003 1008
25. S. Dementin, A. Bouhss, G. Auger, C. Parquet, D. Mengin-Lecreulx, O. Dideberg, J. van Heijenoort, and D. Blanot Evidence of a functional requirement for a carbamoylated lysine residue in MurD, MurE and MurF synthetases as established by chemical rescue experiments Eur. J. Biochem. 268 2001 5800 5807 (Pubitemid 33079314)
26. A.J. O'Neill Staphylococcus aureus SH1000 and 8325-4: comparative genome sequences of key laboratory strains in staphylococcal research Lett. Appl. Microbiol. 51 2010 358 361
27. A.J. O'Neill, J.M. Bostock, A.M. Moita, and I. Chopra Antimicrobial activity and mechanisms of resistance to cephalosporin P1, an antibiotic related to fusidic acid J. Antimicrob. Chemother. 50 2002 839 848 (Pubitemid 36032803)
28. E. Shapiro, and F. Baneyx Stress-based identification and classification of antibacterial agents: second-generation Escherichia coli reporter strains and optimization of detection Antimicrob. Agents Chemother. 46 2002 2490 2497 (Pubitemid 34793454)
29. P.A. Wayne Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically approved standard ninth ed. 2012 Clinical and Laboratory Standards Institute CLSI Document M07-A9
30. R.A. Dixon, and I. Chopra Leakage of periplasmic proteins from Escherichia coli mediated by polymyxin B nonapeptide Antimicrob. Agents Chemother. 29 1986 781 788 (Pubitemid 16118312)
31. α,β-butenolides J. Org. Chem. 7 1942 444 456
32. P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson, and M.T. Stahl Conformer generation with OMEGA: algorithm and validation using high quality structures from the protein databank and the Cambridge structural database J. Chem. Inf. Model. 50 2010 572 584
33. P.C. Hawkins, and A. Nicholis Conformer generation with OMEGA: learning from the data set and the analysis of failures J. Chem. Inf. Model. 52 2012 2919 2936
34. M. McGann FRED pose prediction and virtual screening accuracy J. Chem. Inf. Model. 51 2011 578 596 2
35. G.B. McGaughey, R.P. Sheridan, C.I. Bayly, J.C. Culberson, C. Kreatsolas, S. Lindsley, V. Maiorov, J.-F. Truchon, and W.D. Cornell Comparison of topological, shape, and docking methods in virtual screening J. Chem. Inf. Model. 47 2007 1504 1519 (Pubitemid 47210053)