Computer-aided identification of novel 3,5-substituted rhodanine derivatives with activity against Staphylococcus aureus DNA gyrase

Bioorganic and Medicinal Chemistry

Volumn 22, Issue 7, 2014, Pages 2176-2187

  Werner, Malela M ^a   Li, Zhiyu ^a   Zauhar, Randy J ^a  

^a UNIVERSITY OF THE SCIENCES   (United States)

Author keywords

Antimicrobial; Docking; Interaction frequency; Molecular dynamics; Multiple linear regression model; Rhodanine derivatives; Staphylococcus aureus DNA gyrase

Indexed keywords

2 [5 [[5 (2,5 DICHLOROPHENYL)FURAN 2 YL]METHYLIDENE] 4 OXO 2 THIOXO 1,3 THIAZOLIDIN 3 YL]BUTANEDIOIC ACID; 3 (2 ETHYLPHENYL) 5 (3 HYDROXYBENZYLIDENE) 2 THIOXO 1,3 THIAZOLIDIN 4 ONE; 3 [5 (2 CHLOROBENZYLIDENE) 4 OXO 2 THIOXO 1,3 THIAZOLIDIN 3 YL] 3 PHENYLPROPANOIC ACID; DNA TOPOISOMERASE (ATP HYDROLYSING); GYRASE INHIBITOR; NOVOBIOCIN; UNCLASSIFIED DRUG; RHODANINE;

ANTIBACTERIAL ACTIVITY; ARTICLE; BINDING AFFINITY; COMPUTER ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA SUPERCOILING; DRUG IDENTIFICATION; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; ENZYME INHIBITION; LIGAND BINDING; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; STAPHYLOCOCCUS AUREUS; STRUCTURAL HOMOLOGY; THERMUS THERMOPHILUS; VALIDATION PROCESS; VIRTUAL REALITY; CHEMICAL STRUCTURE; CHEMISTRY; DOSE RESPONSE; DRUG EFFECTS; ENZYMOLOGY; METABOLISM; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; STRUCTURE ACTIVITY RELATION; SYNTHESIS;

BACTERIA (MICROORGANISMS); METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS AUREUS; THERMUS THERMOPHILUS;

DNA GYRASE; DOSE-RESPONSE RELATIONSHIP, DRUG; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; RHODANINE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84897395097     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2014.02.020     Document Type: Article

References (61)

1. A. Waness J. Glob. Infect. Dis. 2 2010 49
2. H.W. Boucher, and G.R. Corey Clin. Infect. Dis. 46 2008 S344
3. H. Boucher, L.G. Miller, and R.R. Razonable Clin. Infect. Dis. 51 2010 S183
4. M.R. Klevens, M.A. Morrison, J. Nadle, S. Petit, K. Gershman, S. Ray, L.H. Harrison, R. Lynfield, G. Dumyati, J.M. Townes, A.S. Craig, E.R. Zell, G.E. Fosheim, L.K. McDougal, R.B. Carey, and S.K. Fridkin J. Am. Med. Assoc. 298 2007 1763
5. G.A. Filice, J.A. Nyman, C. Lexau, C.H. Lees, L.A. Bockstedt, K. Como-Sabetti, L.J. Lesher, and R. Lynfield Infect. Control Hosp. Epidemiol. 31 2010 365
6. A. Sugino, P.N. Higgins, P.O. Brown, C.L. Peebles, and N.R. Cozzarelli Proc. Natl. Acad. Sci. U.S.A. 75 1978 4838
7. C. Sissi, and M. Palumbo Cell. Mol. Life Sci. 67 2010 2001
8. J. Roca Nucleic Acids Res. 37 2008 721
9. A. Gubaev, and D. Klostermeier Proc. Natl. Acad. Sci. U.S.A. 108 2011 14085
10. J. Heddle, and A. Maxwell Antimicrob. Agents Chemother. 46 2002 1805
11. H. Yoshida, M. Bogaki, M. Nakamura, L.M. Yamanaka, and S. Nakamura Antimicrob. Agents Chemother. 35 1991 1647
12. A. Pantel, S. Petrella, N. Veziris, F. Brossier, S. Bastian, V. Jarlier, C. Mayer, and A. Aubry Antimicrob. Agents Chemother. 56 2012 1990
13. D. Lafitte, V. Lamour, P.O. Tsvetkov, A.A. Makarov, M. Klich, P. Deprez, D. Moras, C. Briand, and R. Gilli Biochemistry 41 2002 7217
14. R.P. Cox, E.L. Foltz, S. Raymond, and R. Drewyer N. Eng. J. Med. 261 1959 139
15. N. Nakada, H. Gmunder, T. Hirata, and M. Arisawa Antimicrob. Agents Chemother. 38 1994 1966
16. H. Gradisar, P. Pristovsek, A. Plaper, and R. Jerala J. Med. Chem. 50 2007 264
17. B.A. Sherer, K. Hull, O. Green, G. Basarab, S. Hauck, P. Hill, J.T. Lock, G. Mullen, S. Bist, J. Bryant, A. Boriack-Sjodin, J. Read, N. Degrace, M. Uria-Nickelsen, R.N. Illingworth, and A.E. Eakin Bioorg. Med. Chem. Lett. 21 2011 7416
18. M. Oblak, M. Kotnik, and T. Solmajer Curr. Med. Chem. 14 2007 2033
19. L. Xu, C. Zheng, L. Sun, J. Miao, and H. Piao Eur. J. Med. Chem. 48 2012 174
20. Z. Chen, C. Zheng, L. Sun, and H. Piao Eur. J. Med. Chem. 45 2010 5739
21. M. Brvar, A. Perdih, V. Hodnik, M. Renko, G. Anderluh, R. Jerala, and T. Solmajer Bioorg. Med. Chem. 20 2012 2572
22. R.J. Zauhar, G. Moyna, L. Tian, Z. Li, and W.J. Welsh J. Med. Chem. 46 2003 5674
23. V. Lamour, L. Hoermann, J.M. Jeltsch, P. Oudet, and D. Moras J. Biol. Chem. 277 2002 18947
24. Glide, Version 5.8, Schrödinger, LLC, New York, NY, 2012.
25. R.A. Friesner, J.L. Banks, R.B. Murphy, T.A. Halgren, J.J. Klicic, D.T. Mainz, M.P. Repasky, E.H. Knoll, M. Shelley, J.K. Perry, D.E. Shaw, P. Francis, and P.S. Shenkin J. Med. Chem. 47 2004 1739
26. T.A. Halgren, R.B. Murphy, R.A. Friesner, H.S. Beard, L.L. Frye, W.T. Pollard, and J.L. Banks J. Med. Chem. 47 2004 1750
27. R.A. Friesner, R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, and D. Mainz J. Med. Chem. 49 2006 6177
28. G. Jones, P. Willett, R.C. Glen, A.R. Leach, and R. Taylor J. Mol. Biol. 267 1997 727
29. M.L. Verdonk, J.C. Cole, M.J. Hartshorn, C.W. Murray, and R.D. Taylor Proteins 52 2003 609
30. M. Webb Proc. Natl. Acad. Sci. U.S.A. 89 1992 4884
31. The Pymol Molecular Graphics System, Version 1.5.0.4 Schrödinger LLC.
32. Induced Fit Docking protocol 2013-2, Glide Version 5.9 Prime Version 3.2, Schrodinger, LLC, New York, NY 2013.
33. W. Sherman, T. Day, M.P. Jacobson, and R.A. Friesner J. Med. Chem. 49 2006 534
34. W. Sherman, H.S. Beard, and R. Farid Chem. Biol. Drug Des. 67 2006 83
35. QM-Polarized Ligand Docking Protocol 2013-2; Glide Version 5.9, Jaguar Version 8.0, QSite version 5.9, Schrodinger, LLC, New York, NY, 2013.
36. A.E. Cho, V. Guallar, B. Berne, and R.A. Friesner J. Comput. Chem. 26 2005 915
37. Desmond Molecular Dynamics System, Version 3.1, D. E. Shaw Research, New York, NY, 2012. Maestro-Desmond Interoperability Tools, Version, 3.1, Schödinger, New York, NY, 2012.
38. Desmond Molecular Dynamics System, Version 3.5, D. E. Shaw Research, New York, NY, 2013. Maestro-Desmond Interoperability Tools, version 3.5, Schrödinger, New York, NY, 2013.
39. QikProp, Version 3.4, Schrödinger, LLC, New York, NY, 2011.
40. C.A. Lipinski, F. Lombardo, B.W. Dominy, and P.J. Feeney Adv. Drug Del. Rev. 46 2001 3
41. Strike, Version 2.3, Schrödinger, LLC, New York, NY, 2013.
42. J.J. Irwin, and B.K. Shoichet J. Chem. Inf. Model. 45 2005 177
43. C. Sissi, and M. Palumbo Nucleic Acids Res. 37 2009 702
44. K. Barrett-Bee, and P. Pinder J. Antimicrob. Chemother. 33 1994 1165
45. Lafitte, D.; Lamour, V.; Tsvetkov, P. O.; Makarov, A. A.; Klich, M.; Deprez, P.; Moras, D.; Briand, C.; Gilli, R. 2002, 41, 7217-7223.
46. C.H. Gross, J.D. Parsons, T.H. Grossman, P.S. Charifson, S. Bellon, J. Jernee, M. Dwyer, S.P. Chambers, W. Markland, M. Botfield, and S.A. Raybuck Antimicrob. Agents Chemother. 47 2003 1037
47. D. Ince, X. Zhang, and D.C. Hooper Antimicrob. Agents Chemother. 47 2003 1410
48. N.J. De Souza, S.V. Gupte, P.K. Deshpande, V.N. Desai, S.B. Bhawsar, R.D. Yeole, M.C. Shukla, J. Strahilevitz, D.C. Hooper, B. Bozdogan, P.C. Appelbaum, M.R. Jacobs, N. Shetty, M.V. Patel, R. Jha, and H.F. Khorakiwala J. Med. Chem. 48 2005 5232
49. J. Strahilevitz, and D.C. Hooper Antimicrob. Agents Chemother. 49 2005 1949
50. J.S. Edward, and B.O. Palsson Proc. Natl. Acad. Sci. U.S.A. 97 2000 5528
51. LigPrep, Version 2.4, Schrödinger, LLC, New York, NY, 2010.
52. Schrödinger Suite 2010 Protein Preparation Wizard; Epik Version 2.1, Schrödinger, LLC, New York, NY, 2010; Impact Version 5.6, Schrödinger, LLC, New York, NY, 2010; Prime Version 2.2, Schrödinger, LLC, New York, NY, 2010.
53. Schrödinger Suite 2012 Protein Preparation Wizard; Epik Version 2.3, Schrödinger, LLC, New York, NY, 2012; Impact Version 5.8, Schrödinger, LLC, New York, NY, 2012; Prime Version 3.1, Schrödinger, LLC, New York, NY, 2012.
54. J.R. Zgoda, and J.R. Porter Pharm. Biol. 39 2001 221
55. R.J. Lambert Lett. Appl. Microbiol. 26 1998 288
56. J. Latimer, S. Forbes, and A.J. McBain Antimicrob. Agents Chemother. 56 2012 3092
57. U. Reischl, H. Linde, M. Metz, B. Leppmeier, and N. Lehn J. Clin. Microbiol. 38 2000 2429
58. A. Huletsky, R. Giroux, V. Rossbach, M. Gagnon, M. Vaillancourt, M. Bernier, F. Gagnon, K. Truchon, M. Bastien, F.J. Picard, A. van Belkum, M. Ouellette, P.H. Roy, and M.G. Bergeron J. Clin. Microbiol. 42 2004 1875
59. Maestro, Version 9.5, Schrödinger, LLC, New York, NY 2013.
60. U. Seybold, E.V. Kourbatova, J.G. Johnson, S.J. Halvosa, Y.F. Wang, M.D. King, S.M. Ray, and H.M. Blumberg Clin. Infect. Dis. 42 2006 647
61. M.K. Kristen, O.C. Stine, J.K. Johnson, E.N. Perencevich, M.D. Shardell, A.J. Lesse, F.M. Gordin, M.W. Climo, and M.C. Roghmann Diagn. Microbiol. Infect. Dis. 70 2011 285