Combining in silico and biophysical methods for the development of pseudomonas aeruginosa quorum sensing inhibitors: An alternative approach for structure-based drug design

Journal of Medicinal Chemistry

Volumn 56, Issue 21, 2013, Pages 8656-8664

  Sahner, J Henning ^a   Brengel, Christian ^a   Storz, Michael P ^a   Groh, Matthias ^a   Plaza, Alberto ^a   Müller, Rolf ^a   Hartmann, Rolf W ^a  

^a SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL ENZYME; CARBOXYLIC ACID DERIVATIVE; POLYCYCLIC AROMATIC HYDROCARBON DERIVATIVE; PROTEIN PQSD; QUORUM SENSING INHIBITOR; THIOPHENE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; COVALENT BOND; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG POTENCY; DRUG SELECTIVITY; ELECTROSPRAY MASS SPECTROMETRY; ENZYME ACTIVE SITE; ENZYME INHIBITION; IC 50; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR DOCKING; NONHUMAN; PROTON NUCLEAR MAGNETIC RESONANCE; PSEUDOMONAS AERUGINOSA; QUORUM SENSING; STEREOSPECIFICITY; STRUCTURE ACTIVITY RELATION; SURFACE PLASMON RESONANCE; X RAY CRYSTALLOGRAPHY;

CARBOXYLIC ACIDS; DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG DESIGN; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PSEUDOMONAS AERUGINOSA; QUORUM SENSING; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; THIOPHENES;

EID: 84887968536     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm401102e     Document Type: Article

References (25)

1. Wagner, G.; Hyberts, S. G.; Havel, T. F. NMR structure determination in solution: a critique and comparison with X-ray crystallography Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 167-198
2. Davis, A. M.; Teague, S. J.; Kleywegt, G. J. Application and limitations of X-ray crystallographic Data in structure-based ligand and drug design Angew. Chem., Int. Ed. 2003, 42, 2718-2736
3. Boström, J. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools J. Comput.-Aided Mol. Des. 2001, 15, 1137-1152
4. Xiao, G.; Dézièl, E.; He, J.; Lépine, F.; Lesic, B.; Castonguay, M.-H.; Milot, S.; Tampakaki, A. P.; Stachel, S. E.; Rahme, L. G. MvfR, a key Pseudomonas aeruginosa pathogenicity LTTR-class regulatory protein, has dual ligands Mol. Microbiol. 2006, 62, 1689-1699
5. For a recent review see Dubern, J.-F.; Diggle, S. P. Quorum sensing by 2-alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species Mol. Biosyst. 2008, 4, 882-888
6. Bera, A. K.; Atanasova, V.; Robinson, H.; Eisenstein, E.; Coleman, J. P.; Pesci, E. C.; Parsons, J. F. Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate Biochemistry 2009, 48, 8644-8655
7. Storz, M. P.; Maurer, C. K.; Zimmer, C.; Wagner, N.; Brengel, C.; de Jong, J. C.; Lucas, S.; Müsken, M.; Häussler, S.; Steinbach, A.; Hartmann, R. W. Validation of PqsD as an anti-biofilm target in Pseudomonas aeruginosa by development of small-molecule inhibitors J. Am. Chem. Soc. 2012, 134, 16143-16146
8. Gomez, M. I.; Prince, A. Opportunistic infections in lung disease: Pseudomonas infections in cystic fibrosis Curr. Opin. Pharmacol. 2007, 7, 244-251
9. Hakki, M.; Limaye, A. P.; Kim, H. W.; Kirby, K. A.; Corey, L.; Boeckh, M. Invasive Pseudomonas aeruginosa infections: high rate of recurrence and mortality after hematopoietic cell transplantation Bone Marrow Transplant. 2007, 39, 687-693
10. Asboe, D.; Gant, V.; Aucken, H. M.; Moore, D. A.; Umasankar, S.; Bingham, J. S.; Kaufmann, M. E.; Pitt, T. L. Persistence of Pseudomonas aeruginosa strains in respiratory infection in AIDS patients AIDS (Hagerstown, MD, U. S.) 1998, 12, 1771-1775
11. Pistorius, D.; Ullrich, A.; Lucas, S.; Hartmann, R. W.; Kazmaier, U.; Müller, R. Biosynthesis of 2-alkyl-4(1 H)-quinolones in Pseudomonas aeruginosa: potential for therapeutic interference with pathogenicity ChemBioChem 2011, 12, 850-853
12. Sahner, J. H.; Groh, M.; Negri, M.; Haupenthal, J.; Hartmann, R. W. Novel small moleucle inhibitors targeting the "switch region" of bacterial RNAP: structure-based optimization of a virtual screening hit Eur. J. Med. Chem. 2013, 65, 223-231
13. Hentzer, M.; Givskov, M. Pharmacological inhibition of quorum sensing for treatment of chronic bacterial infections J. Clin. Invest. 2003, 112, 1300-1307
14. Storz, M. P.; Brengel, C.; Weidel, E.; Hoffmann, M.; Empting, M.; Steinbach, A.; Müller, R.; Hartmann, R. W. unpublished results.
15. O'Shea, R.; Moser, H. E. Physicochemical properties of antibacterial compounds: implications for drug discovery J. Med. Chem. 2008, 51, 2871-2878
16. Mayer, M.; Meyer, B. Characterization of ligand binding by saturation transfer difference NMR spectroscopy Angew. Chem., Int. Ed. 1999, 38, 1784-1788
17. Henise, J. C.; Taunton, J. Irreversible Nek2 kinase inhibitors with cellular activity J. Med. Chem. 2011, 54, 4133-4146
18. Copeland, R. A.; Pompliano, D. L.; Meek, T. D. Drug-target residence time and its implications for lead optimization Nature Rev. Drug Discovery 2006, 5, 730-739
19. Hartmann, H.; Liebscher, J. A simple method for the synthesis of 5-aryl-3-amino-2-alkoxycarbonylthiophenes Synthesis 1984, 275-276
20. Fabis, F.; Jolivet-Fouchet, S.; Robba, M.; Landelle, H.; Rault, S. Thiaisatoic anhydrides: efficient synthesis under microwave heating conditions and study of their reactivity Tetrahedron 1998, 54, 10789-10800
21. Foulon, L.; Braud, E.; Fabis, F.; Lancelot, J. C.; Rault, S. Synthesis and combinatorial approach of the reactivity of 6-and 7-arylthieno[3, 2- d ][1, 3]oxazine-2, 4-diones Tetrahedron 2003, 59, 10051-10057
22. Le Foulon, F. X.; Braud, E.; Fabis, F.; Lancelot, J. C.; Rault, S. Solution-phase parallel synthesis of a 1140-member ureidothiophene carboxylic acid library J. Comb. Chem. 2005, 7, 253-257
23. Haupenthal, J.; Hüsecken, K.; Negri, M.; Maurer, C. K.; Hartmann, R. W. Influence of DNA template choice on transcription and inhibition of E. Coli RNA polymerase Antimicrob. Agents Chemother. 2012, 56, 4536-4539
24. Molecular Operating Environment (MOE), 2010.10; Chemical Computing Group Inc.: 1010 Sherbooke Street West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2010.
25. Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J. Comput. Chem. 2009, 31, 455-461