A small molecule discrimination map of the antibiotic resistance kinome

Chemistry and Biology

Volumn 18, Issue 12, 2011, Pages 1591-1601

  Shakya, Tushar ^a   Stogios, Peter J ^b,c   Waglechner, Nicholas ^a   Evdokimova, Elena ^b,c   Ejim, Linda ^a   Blanchard, Jan E ^d   McArthur, Andrew G ^e   Savchenko, Alexei ^b,c   Wright, Gerard D ^a  

^a MCMASTER UNIVERSITY   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c Center for Structural Genomics of Infectious Diseases (CSGID)   (Canada)

^d McMaster University   (Canada)

^e Andrew McArthur Consulting   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE 2'' PHOSPHOTRANSFERASE; AMINOGLYCOSIDE 2''-PHOSPHOTRANSFERASE; ANTIINFECTIVE AGENT; PHOSPHOTRANSFERASE; PROTEIN KINASE; PROTEIN KINASE INHIBITOR; QUERCETIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BINDING SITE; CHEMISTRY; DRUG DESIGN; DRUG EFFECT; ENZYME ACTIVATION; KINETICS; METABOLISM; MOLECULAR LIBRARY; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

ANTI-BACTERIAL AGENTS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; DRUG RESISTANCE, BACTERIAL; ENZYME ACTIVATION; KINETICS; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY; QUERCETIN; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

IVA;

EID: 84555196910     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2011.10.018     Document Type: Article

References (59)

1. M. Akova, Y. Yang, and D.M. Livermore Interactions of tazobactam and clavulanate with inducibly- and constitutively-expressed Class I beta-lactamases J. Antimicrob. Chemother. 25 1990 199 208 (Pubitemid 20085799)
2. G. Altekar, S. Dwarkadas, J.P. Huelsenbeck, and F. Ronquist Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference Bioinformatics 20 2004 407 415 (Pubitemid 38262773)
3. R.H. Baltz Marcel Faber Roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration? J. Ind. Microbiol. Biotechnol. 33 2006 507 513 (Pubitemid 43876111)
4. S.C. Bischoff Quercetin: potentials in the prevention and therapy of disease Curr. Opin. Clin. Nutr. Metab. Care 11 2008 733 740
5. D.D. Boehr, W.S. Lane, and G.D. Wright Active site labeling of the gentamicin resistance enzyme AAC(6′)-APH(2″) by the lipid kinase inhibitor wortmannin Chem. Biol. 8 2001 791 800 (Pubitemid 32752458)
6. D.D. Boehr, P.R. Thompson, and G.D. Wright Molecular mechanism of aminoglycoside antibiotic kinase APH(3′)-IIIa: roles of conserved active site residues J. Biol. Chem. 276 2001 23929 23936
7. E.R. Choffnes, D.A. Relman, and A. Mack Antibiotic Resistance: Implications for Global Health and Novel Intervention Strategies 2010 National Academy of Sciences Washington
8. M.A. Cooper, and D. Shlaes Fix the antibiotics pipeline Nature 472 2011 32
9. T.P. Cushnie, and A.J. Lamb Recent advances in understanding the antibacterial properties of flavonoids Int. J. Antimicrob. Agents 38 2011 99 107
10. D.M. Daigle, G.A. McKay, and G.D. Wright Inhibition of aminoglycoside antibiotic resistance enzymes by protein kinase inhibitors J. Biol. Chem. 272 1997 24755 24758 (Pubitemid 27415642)
11. D.M. Daigle, G.A. McKay, P.R. Thompson, and G.D. Wright Aminoglycoside antibiotic phosphotransferases are also serine protein kinases Chem. Biol. 6 1999 11 18 (Pubitemid 29363041)
12. A.C. Dar, and K.M. Shokat The evolution of protein kinase inhibitors from antagonists to agonists of cellular signaling Annu. Rev. Biochem. 80 2011 769 795
13. S.R. Eddy A new generation of homology search tools based on probabilistic inference Genome Inform. 23 2009 205 211
14. R.C. Edgar MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 2004 113
15. L. Ejim, M.A. Farha, S.B. Falconer, J. Wildenhain, B.K. Coombes, M. Tyers, E.D. Brown, and G.D. Wright Combinations of antibiotics and nonantibiotic drugs enhance antimicrobial efficacy Nat. Chem. Biol. 7 2011 348 350
16. M.A. Fabian, W.H. Biggs 3rd, D.K. Treiber, C.E. Atteridge, M.D. Azimioara, M.G. Benedetti, T.A. Carter, P. Ciceri, P.T. Edeen, and M. Floyd A small molecule-kinase interaction map for clinical kinase inhibitors Nat. Biotechnol. 23 2005 329 336 (Pubitemid 41094421)
17. O. Fedorov, B. Marsden, V. Pogacic, P. Rellos, S. Müller, A.N. Bullock, J. Schwaller, M. Sundström, and S. Knapp A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases Proc. Natl. Acad. Sci. USA 104 2007 20523 20528
18. M.A. Fischbach, and C.T. Walsh Antibiotics for emerging pathogens Science 325 2009 1089 1093
19. D.H. Fong, C.T. Lemke, J. Hwang, B. Xiong, and A.M. Berghuis Structure of the antibiotic resistance factor spectinomycin phosphotransferase from Legionella pneumophila J. Biol. Chem. 285 2010 9545 9555
20. A. Gazit, P. Yaish, C. Gilon, and A. Levitzki Tyrphostins I: synthesis and biological activity of protein tyrosine kinase inhibitors J. Med. Chem. 32 1989 2344 2352 (Pubitemid 19245898)
21. M.N. Gwynn, A. Portnoy, S.F. Rittenhouse, and D.J. Payne Challenges of antibacterial discovery revisited Ann. N Y Acad. Sci. 1213 2010 5 19
22. J.H. Hanke, J.P. Gardner, R.L. Dow, P.S. Changelian, W.H. Brissette, E.J. Weringer, B.A. Pollok, and P.A. Connelly Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. Study of Lck- and FynT-dependent T cell activation J. Biol. Chem. 271 1996 695 701
23. W.C. Hon, G.A. McKay, P.R. Thompson, R.M. Sweet, D.S. Yang, G.D. Wright, and A.M. Berghuis Structure of an enzyme required for aminoglycoside antibiotic resistance reveals homology to eukaryotic protein kinases Cell 89 1997 887 895 (Pubitemid 27513515)
24. J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755 (Pubitemid 32851390)
25. J.E. Hugonnet, L.W. Tremblay, H.I. Boshoff, C.E. Barry 3rd, and J.S. Blanchard Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis Science 323 2009 1215 1218
26. L. Kalan, and G.D. Wright Antibiotic adjuvants: multicomponent anti-infective strategies Expert Rev. Mol. Med. 13 2011 e5
27. N. Kannan, S.S. Taylor, Y. Zhai, J.C. Venter, and G. Manning Structural and functional diversity of the microbial kinome PLoS Biol. 5 2007 e17
28. M.W. Karaman, S. Herrgard, D.K. Treiber, P. Gallant, C.E. Atteridge, B.T. Campbell, K.W. Chan, P. Ciceri, M.I. Davis, and P.T. Edeen A quantitative analysis of kinase inhibitor selectivity Nat. Biotechnol. 26 2008 127 132
29. G.S. Kelly Quercetin. Monograph Altern. Med. Rev. 16 2011 172 194
30. Z.A. Knight, H. Lin, and K.M. Shokat Targeting the cancer kinome through polypharmacology Nat. Rev. Cancer 10 2010 130 137
31. R. Labia, A. Morand, V. Lelievre, D. Mattioni, and A. Kazmierczak Sulbactam: biochemical factors involved in its synergy with ampicillin Rev. Infect. Dis. 8 Suppl 5 1986 S496 S502
32. D.A. Leigh, K. Bradnock, and J.M. Marriner Augmentin (amoxycillin and clavulanic acid) therapy in complicated infections due to beta-lactamase producing bacteria J. Antimicrob. Chemother. 7 1981 229 236 (Pubitemid 11159350)
33. J.J. Liao Molecular targeting of protein kinases to optimize selectivity and resistance profiles of kinase inhibitors Curr. Top. Med. Chem. 7 2007 1332 1335 (Pubitemid 47484762)
34. D.M. Livermore, S. Mushtaq, M. Warner, C. Miossec, and N. Woodford NXL104 combinations versus Enterobacteriaceae with CTX-M extended-spectrum beta-lactamases and carbapenemases J. Antimicrob. Chemother. 62 2008 1053 1056
35. S. Mahajan, S. Ghosh, E.A. Sudbeck, Y. Zheng, S. Downs, M. Hupke, and F.M. Uckun Rational design and synthesis of a novel anti-leukemic agent targeting Bruton's tyrosine kinase (BTK), LFM-A13 [alpha-cyano-beta-hydroxy- beta-methyl-N-(2, 5-dibromophenyl)propenamide] J. Biol. Chem. 274 1999 9587 9599
36. S.L. McGovern, and B.K. Shoichet Kinase inhibitors: not just for kinases anymore J. Med. Chem. 46 2003 1478 1483 (Pubitemid 36512711)
37. J.R. Miller, S. Dunham, I. Mochalkin, C. Banotai, M. Bowman, S. Buist, B. Dunkle, D. Hanna, H.J. Harwood, and M.D. Huband A class of selective antibacterials derived from a protein kinase inhibitor pharmacophore Proc. Natl. Acad. Sci. USA 106 2009 1737 1742
38. D. Nurizzo, S.C. Shewry, M.H. Perlin, S.A. Brown, J.N. Dholakia, R.L. Fuchs, T. Deva, E.N. Baker, and C.A. Smith The crystal structure of aminoglycoside-3′-phosphotransferase-IIa, an enzyme responsible for antibiotic resistance J. Mol. Biol. 327 2003 491 506 (Pubitemid 36298717)
39. F. Perez-Vizcaino, J. Duarte, R. Jimenez, C. Santos-Buelga, and A. Osuna Antihypertensive effects of the flavonoid quercetin Pharmacol. Rep. 61 2009 67 75
40. N.G. Pon, and R.J. Bondar A direct spectrophotometric assay for pyruvate kinase Anal. Biochem. 19 1967 272 279
41. F. Ronquist, and J.P. Huelsenbeck MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 2003 1572 1574 (Pubitemid 37038874)
42. E.D. Scheeff, and P.E. Bourne Structural evolution of the protein kinase-like superfamily PLoS Comput. Biol. 1 2005 e49
43. M. Spitzer, E. Griffiths, K.M. Blakely, J. Wildenhain, L. Ejim, L. Rossi, G. De Pascale, J. Curak, E. Brown, M. Tyers, and G.D. Wright Cross-species discovery of syncretic drug combinations that potentiate the antifungal fluconazole Mol. Syst. Biol. 7 2011 499
44. P.J. Stogios, T. Shakya, E. Evdokimova, A. Savchenko, and G.D. Wright Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme J. Biol. Chem. 286 2011 1966 1975
45. F. Teillet, A. Boumendjel, J. Boutonnat, and X. Ronot Flavonoids as RTK inhibitors and potential anticancer agents Med. Res. Rev. 28 2008 715 745
46. S.A. Testero, J.F. Fisher, and S. Mobashery Lactam Antibiotics D.J. Abraham, D.P. Rotella, Burger's Medicinal Chemistry, Drug Discovery and Development 2010 Wiley & Sons New York 259 404
47. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680 (Pubitemid 24354800)
48. P.R. Thompson, D.D. Boehr, A.M. Berghuis, and G.D. Wright Mechanism of aminoglycoside antibiotic kinase APH(3′)-IIIa: role of the nucleotide positioning loop Biochemistry 41 2002 7001 7007 (Pubitemid 34575672)
49. M. Toth, H. Frase, N.T. Antunes, C.A. Smith, and S.B. Vakulenko Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2″- IVa Protein Sci. 19 2010 1565 1576
50. P. Traxler, J. Green, H. Mett, U. Séquin, and P. Furet Use of a pharmacophore model for the design of EGFR tyrosine kinase inhibitors: isoflavones and 3-phenyl-4(1H)-quinolones J. Med. Chem. 42 1999 1018 1026 (Pubitemid 29153431)
51. C.J. Vlahos, W.F. Matter, K.Y. Hui, and R.F. Brown A specific inhibitor of phosphatidylinositol 3-kinase, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4- one (LY294002) J. Biol. Chem. 269 1994 5241 5248
52. W.H. Ward, P.N. Cook, A.M. Slater, D.H. Davies, G.A. Holdgate, and L.R. Green Epidermal growth factor receptor tyrosine kinase. Investigation of catalytic mechanism, structure-based searching and discovery of a potent inhibitor Biochem. Pharmacol. 48 1994 659 666
53. S. Whelan, and N. Goldman A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach Mol. Biol. Evol. 18 2001 691 699 (Pubitemid 32372940)
54. O.L. Woodman, and E.Ch. Chan Vascular and anti-oxidant actions of flavonols and flavones Clin. Exp. Pharmacol. Physiol. 31 2004 786 790 (Pubitemid 39556854)
55. G.D. Wright The antibiotic resistome: the nexus of chemical and genetic diversity Nat. Rev. Microbiol. 5 2007 175 186 (Pubitemid 46291277)
56. G.D. Wright, and P.R. Thompson Aminoglycoside phosphotransferases: proteins, structure, and mechanism Front. Biosci. 4 1999 D9 D21
57. P.G. Young, R. Walanj, V. Lakshmi, L.J. Byrnes, P. Metcalf, E.N. Baker, S.B. Vakulenko, and C.A. Smith The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2″- phosphotransferase-IIa [APH(2″)-IIa] provide insights into substrate selectivity in the APH(2″) subfamily J. Bacteriol. 191 2009 4133 4143
58. J.H. Zhang, T.D. Chung, and K.R. Oldenburg A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays J. Biomol. Screen. 4 1999 67 73 (Pubitemid 29278954)
59. J. Zhang, P.L. Yang, and N.S. Gray Targeting cancer with small molecule kinase inhibitors Nat. Rev. Cancer 9 2009 28 39