Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2′-F-c-di-GMP

Bioorganic and Medicinal Chemistry

Volumn 21, Issue 14, 2013, Pages 4396-4404

  Zhou, Jie ^a   Watt, Sarah ^a   Wang, Jingxin ^a   Nakayama, Shizuka ^a   Sayre, David A ^a   Lam, Yiu Fai ^a   Lee, Vincent T ^a   Sintim, Herman O ^a  

^a Bldg 142   (United States)

Author keywords

2 F c di GMP 2 OMe c di GMP; 2 H c di GMP; C di GMP; DGC; DOSY; G quadruplex; PDE; PilZ; Polymorphism

Indexed keywords

2' FLUORINE CYCLIC DI GMP; 2' HYDROGEN CYCLIC DI GMP; 2' METHOXY CYCLIC DI GMP; BINDING PROTEIN; CYCLIC DI GMP; CYCLIC GMP; DIGUANYLATE CYCLASE; GUANYLATE CYCLASE; PHOSPHODIESTERASE; PILZ CONTAINING PROTEIN; POTASSIUM SALT; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING ASSAY; BINDING COMPETITION; CELL MEMBRANE PERMEABILITY; CONTROLLED STUDY; DIFFUSSION ORDERED SPECTROSCOPY; ENZYME INHIBITION; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACID SYNTHESIS; NUCLEOTIDE BINDING SITE; PROTEIN BINDING; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; SPECTROSCOPY; STRUCTURE ANALYSIS;

ALLOSTERIC REGULATION; BACTERIA; CYCLIC GMP; ENZYME INHIBITORS; ESCHERICHIA COLI PROTEINS; FLUORINE; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR STRUCTURE; PHOSPHORUS-OXYGEN LYASES;

BACTERIA (MICROORGANISMS);

EID: 84879012079     PISSN: 09680896     EISSN: 14643391     Source Type: Journal    
DOI: 10.1016/j.bmc.2013.04.050     Document Type: Article

References (65)

1. P. Ross, H. Weinhouse, Y. Aloni, D. Michaeli, P. Weinberger-Ohana, R. Mayer, S. Braun, E. de Vroom, G.A. van der Marel, H.H. van Boom, and M. Benziman Nature 325 1987 279
2. U. Römling, M. Gomelsky, and M.Y. Galperin Mol. Microbiol. 57 2005 629
3. H. Sondermann, N.J. Shikuma, and F.H. Yildiz Curr. Opin. Microbiol. 15 2012 140
4. P.V. Krasteva, K.M. Giglio, and H. Sondermann Protein Sci. 21 2012 929
5. R.P. Ryan, T. Tolker-Nielsen, and J.M. Dow Trends Microbiol. 20 2012 235
6. U. Römling Environ. Microbiol. 14 2012 1817
7. R. Tamayo, J.T. Pratt, and A. Camilli Annu. Rev. Microbiol. 61 2007 131
8. K.D. Smith, C.A. Shanahan, E.L. Moore, A.C. Simon, and S.A. Strobel Proc. Natl. Acad. Sci. U.S.A. 108 2011 7757
9. C. Chan, R. Paul, D. Samoray, N.C. Amiot, B. Giese, U. Jenal, and T. Schirmer Proc. Natl. Acad. Sci. U.S.A. 101 2004 17084
10. A.J. Schmidt, D.A. Ryjenkov, and M. Gomelsky J. Bacteriol. 187 2005 4774
11. D.A. Ryjenkov, M. Tarutina, O.V. Moskvin, and M. Gomelsky J. Bacteriol. 187 2005 1792
12. K. Jonas, O. Melefors, and U. Römling Future Microbiol. 4 2009 341
13. A.G. Bobrov, O. Kirillina, D.A. Ryjenkov, C.M. Waters, P.A. Price, J.D. Fetherston, D. Mack, W.E. Goldman, M. Gomelsky, and R.D. Perry Mol. Microbiol. 79 2011 533
14. E. Mills, I.S. Pultz, H.D. Kulasekara, and S.I. Miller Cell Microbiol. 13 2011 1122
15. B. Christen, M. Christen, R. Paul, F. Schmid, M. Folcher, P. Jenoe, M. Meuwly, and U. Jenal J. Biol. Chem. 281 2006 32015
16. C.A. Shanahan, B.L. Gaffney, R.A. Jones, and S.A. Strobel J. Am. Chem. Soc. 133 2011 15578
17. K. Furukawa, H. Gu, N. Sudarsan, Y. Hayakawa, M. Hyodo, and R.R. Breaker ACS Chem. Biol. 7 2012 1436
18. J. Wang, J. Zhou, G.P. Donaldson, S. Nakayama, L. Yan, Y.F. Lam, V.T. Lee, and H.O. Sintim J. Am. Chem. Soc. 133 2011 9320
19. Y. Luo, J. Zhou, S.K. Watt, V.T. Lee, T.K. Dayie, and H.O. Sintim Mol. Biosyst. 8 2012 772
20. S.M. Ching, W.J. Tan, K.L. Chua, and Y. Lam Bioorg. Med. Chem. 18 2010 6657
21. I. Kiburu, A. Shurer, L. Yan, and H.O. Sintim Mol. Biosyst. 4 2008 518
22. B.L. Gaffney, E. Veliath, J. Zhao, and R.A. Jones Org. Lett. 12 2010 3269
23. Z. Zhang, B.L. Gaffney, and R.A. Jones J. Am. Chem. Soc. 126 2004 16700
24. Z. Zhang, S. Kim, B.L. Gaffney, and R.A. Jones J. Am. Chem. Soc. 128 2006 7015
25. S. Nakayama, I. Kelsey, J. Wang, and H.O. Sintim Chem. Commun. (Camb). 47 2011 4766
26. S. Nakayama, I. Kelsey, J. Wang, K. Roelofs, B. Stefane, Y. Luo, V.T. Lee, and H.O. Sintim J. Am. Chem. Soc. 133 2011 4856
27. M. Gentner, M.G. Allan, F. Zaehringer, T. Schirmer, and S. Grzesiek J. Am. Chem. Soc. 134 2012 1019
28. Wassmann, P.; Massa, C.; Zaehringer, F.; Schirmer, T. Unpublished result. (PDB code 2WB4).
29. P. Wassmann, C. Chan, R. Paul, A. Beck, H. Heerklotz, U. Jenal, and T. Schirmer Structure 15 2007 915 (PDB code 2V0N)
30. N. De, M. Pirruccello, P.V. Krasteva, N. Bae, R.V. Raghavan, and H. Sondermann PLoS Biol. 6 2008 e67 (PDB code 3BRE)
31. ref 29. (PDB code 3I5A, 3I5B and 3I5C).
32. Vorobiev, S.; Neely, H.; Seetharaman, J.; Wang, H.; Foote, E. L.; Ciccosanti, C.; Sahdev, S.; Xiao, R.; Acton, T. B.; Montelione, G. T.; Tong, L.; Hunt, J. F. Unpublished result. (PDB code 3IGN).
33. C.Y. Yang, K.H. Chin, M.L. Chuah, Z.X. Liang, A.H. Wang, and S.H. Chou Acta Crystallogr., Sect. D 67 2011 997 (PDB code 3QYY)
34. J.C. Whitney, K.M. Colvin, L.S. Marmont, H. Robinson, M.R. Parsek, and P.L. Howell J. Biol. Chem. 287 2012 23582 (PDB code 4DN0)
35. G. Minasov, S. Padavattan, L. Shuvalova, J.S. Brunzelle, D.J. Miller, A. Baslé, C. Massa, F.R. Collart, T. Schirmer, and W.F. Anderson J. Biol. Chem. 284 2009 13174 (PDB code 2W27)
36. M.V. Navarro, N. De, N. Bae, Q. Wang, and H. Sondermann Structure 17 2009 1104 (PDB code 3HV8 and 3HV9)
37. M.V. Navarro, P.D. Newell, P.V. Krasteva, D. Chatterjee, D.R. Madden, G.A. O′Toole, and H. Sondermann PLoS Biol. 9 2011 e1000588 (PDB code 3PJT and 3PJU)
38. C. Chang, X. Xu, H. Cui, A. Savchenko, A. Yakunin, A. Edwards, and A. Joachimiak J. Mol. Biol. 402 2010 524 (PDB code: 3N3T)
39. J. Benach, S.S. Swaminathan, R. Tamayo, S.K. Handelman, E. Folta-Stogniew, J.E. Ramos, F. Forouhar, H. Neely, J. Seetharaman, A. Camilli, and J.F. Hunt EMBO J. 26 2007 5153 (PDB code 2RDE)
40. J. Habazettl, M.G. Allan, U. Jenal, and S. Grzesiek J. Biol. Chem. 286 2011 14304 (PDB code 2L74)
41. J. Ko, K.S. Ryu, H. Kim, J.S. Shin, J.O. Lee, C. Cheong, and B.S. Choi J. Mol. Biol. 398 2010 97 (PDB code 3KYF and 3KYG)
42. N. De, M.V. Navarro, R.V. Raghavan, and H. Sondermann J. Mol. Biol. 393 2009 619
43. F. Rao, Y. Yang, Y. Qi, and Z.X. Liang J. Bacteriol. 190 2008 3622
44. B.R. Kulasekara, H.D. Kulasekara, M.C. Wolfgang, L. Stevens, D.W. Frank, and S. Lory J. Bacteriol. 188 2006 4037
45. M. Merighi, V.T. Lee, M. Hyodo, Y. Hayakawa, and S. Lory Mol. Microbiol. 65 2007 876
46. U. Remminghorst, and B.H. Rehm FEBS Lett. 580 2006 3883
47. O. Khakshoor, S.E. Wheeler, K.N. Houk, and E.T. Kool J. Am. Chem. Soc. 134 2012 3154
48. E.T. Kool, and H.O. Sintim Chem. Commun. (Camb). 2006 3665
49. M.W. Chen, M. Kotaka, C. Vonrhein, G. Bricogne, F. Rao, M.L. Chuah, D. Svergun, G. Schneider, Z.X. Liang, and J. Lescar J. Bacteriol. 194 2012 4837
50. P. Lubini, W. Zürcher, and M. Egli Chem. Biol. 1 1994 39
51. L.L. Cummins, S.R. Owens, L.M. Risen, E.A. Lesnik, S.M. Freier, D. McGee, C.J. Guinosso, and P.D. Cook Nucleic Acids Res. 23 1995 2019
52. M.J. Frisch Gaussian 09, Revision A02 ed. 2009 Gaussian Inc. Wallingford, CT
53. J.H. Merritt, D.G. Ha, K.N. Cowles, W. Lu, D.K. Morales, J. Rabinowitz, Z. Gitai, and G.A. O'Toole mBio. 1 2010 e00183-10
54. H. Kulasakara, V. Lee, A. Brencic, N. Liberati, J. Urbach, S. Miyata, D.G. Lee, A.N. Neely, M. Hyodo, Y. Hayakawa, F.M. Ausubel, and S. Lory Proc. Natl. Acad. Sci. U.S.A. 103 2006 2839
55. H.O. Sintim, J.A. Smith, J. Wang, S. Nakayama, and L. Yan Future Med. Chem. 2 2010 1005
56. S.A. Rogers, R.W. Huigens, and C. Melander J. Am. Chem. Soc. 131 2009 9868
57. R.W. Huigens, J.J. Richards, G. Parise, T.E. Ballard, W. Zeng, R. Deora, and C. Melander J. Am. Chem. Soc. 129 2007 6966
58. R. Frei, A.S. Breitbach, and H.E. Blackwell Angew. Chem., Int. Ed. 51 2012 5226
59. S. Furukawa, Y. Akiyoshi, G.A. O′Toole, H. Ogihara, and Y. Morinaga Int. J. Food Microbiol. 138 2010 176
60. S. Gamby, V. Roy, M. Guo, J.A. Smith, J. Wang, J.E. Stewart, X. Wang, W.E. Bentley, and H.O. Sintim ACS Chem. Biol. 7 2012 1023
61. M. Guo, S. Gamby, S. Nakayama, J. Smith, and H.O. Sintim Sensors 12 2012 3762
62. V. Singh, G.B. Evans, D.H. Lenz, J.M. Mason, K. Clinch, S. Mee, G.F. Painter, P.C. Tyler, R.H. Furneaux, J.E. Lee, P.L. Howell, and V.L. Schramm J. Biol. Chem. 280 2005 18265
63. V. Singh, W. Shi, S.C. Almo, G.B. Evans, R.H. Furneaux, P.C. Tyler, G.F. Painter, D.H. Lenz, S. Mee, R. Zheng, and V.L. Schramm Biochemistry 45 2006 12929
64. I. Kelsey, S. Nakayama, and H.O. Sintim Bioorg. Med. Chem. Lett. 22 2012 881
65. K.G. Roelofs, J. Wang, H.O. Sintim, and V.T. Lee Proc. Natl. Acad. Sci. U.S.A. 108 2011 15528