Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles

Structure

Volumn 23, Issue 8, 2015, Pages 1470-1481

  Feng, Yu ^a   Degen, David ^a   Wang, Xinyue ^a   Gigliotti, Matthew ^a   Liu, Shuang ^a   Zhang, Yu ^a   Das, Deepankar ^a   Michalchuk, Trevor ^a   Ebright, Yon W ^a   Talaue, Meliza ^b   Connell, Nancy ^b   Ebright, Richard H ^a  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDINE; ANTIBIOTIC AGENT; BACTERIAL RNA; BROMINE; CBR 703; CBR PYRAZOLE DERIVATIVE; HOLOENZYME; NUCLEOTIDYLTRANSFERASE INHIBITOR; PYRAZOLE DERIVATIVE; RNA POLYMERASE; UNCLASSIFIED DRUG; ANTIINFECTIVE AGENT; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; HYDROXYLAMINE; LIGAND; PROTEIN BINDING; RECOMBINANT PROTEIN;

AMINO ACID SUBSTITUTION; ANTIBACTERIAL ACTIVITY; ANTIBIOTIC RESISTANCE; ARTICLE; BINDING SITE; CROSS RESISTANCE; CRYSTAL STRUCTURE; DRUG EFFICACY; DRUG STRUCTURE; ESCHERICHIA COLI; HIGH THROUGHPUT SCREENING; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION; X RAY DIFFRACTION; AMINO ACID SEQUENCE; ANIMAL; ANTAGONISTS AND INHIBITORS; CHEMISTRY; CHLOROCEBUS AETHIOPS; DRUG EFFECTS; DRUG POTENTIATION; ENZYMOLOGY; GENETIC TRANSCRIPTION; GENETICS; HELA CELL LINE; HUMAN; METABOLISM; MOLECULAR GENETICS; MOLECULAR MODEL; MYCOBACTERIUM TUBERCULOSIS; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; VERO CELL LINE; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

AMIDINES; AMINO ACID SEQUENCE; ANIMALS; ANTI-BACTERIAL AGENTS; BINDING SITES; CERCOPITHECUS AETHIOPS; CRYSTALLOGRAPHY, X-RAY; DNA-DIRECTED RNA POLYMERASES; DRUG SYNERGISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HELA CELLS; HUMANS; HYDROXYLAMINES; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PYRAZOLES; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; TRANSCRIPTION, GENETIC; VERO CELLS;

EID: 84938750179     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.06.009     Document Type: Article

References (42)

1. P. Adams, P. Afonine, G. Bunkóczi, V. Chen, I. Davis, N. Echols, J. Head, L. Hung, G. Kapral, R. Grosse-Kunstleve, and et al. PHENIX: a comprehensive Python-based system for macromolecular structure Acta Crystallogr. D Biol. Crystallogr. 66 2010 213 221
2. I. Artsimovitch, C. Chu, A. Lynch, and R. Landick A new class of bacterial RNA polymerase inhibitor affects nucleotide addition Science 302 2003 650 654
3. B. Bae, E. Davis, D. Brown, E. Campbell, S. Wigneshweraraj, and S.A. Darst Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1 Proc. Natl. Acad. Sci. USA 110 2013 19772 19777
4. E. Campbell, N. Korzheva, A. Mustaev, K. Murakami, S. Nair, A. Goldfarb, and S. Darst Structural mechanism for rifampicin inhibition of bacterial RNA polymerase Cell 104 2001 901 912
5. D. Degen, Y. Feng, Y. Zhang, K.Y. Ebright, Y.W. Ebright, M. Gigliotti, H. Vahedian-Movahed, S. Mandal, M. Talaue, N. Connell, and et al. Transcription inhibition by the depsipeptide antibiotic salinamide A Elife 3 2014 e02451
6. R. Ebright RNA Exit Channel-Target and Method for Inhibition of Bacterial RNA Polymerase 2005 World Intellectual Property Organization WO/2005/001034
7. P. Emsley, B. Lohkamp, W. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr. D Biol. Crystallogr. 66 2010 486 501
8. A. Feklistov, V. Mekler, Q. Jiang, L. Westblade, H. Irschik, R. Jansen, A. Mustaev, S. Darst, and R. Ebright Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center Proc. Natl. Acad. Sci. USA 105 2008 14820 14825
9. J. Fralick, and L. Burns-Keliher Additive effect of tolC and rfa mutations on the hydrophobic barrier of the outer membrane of E. coli K-12 J. Bacteriol. 176 1994 6404 6406
10. L. Garibyan, T. Huang, M. Kim, E. Wolff, A. Nguyen, T. Nguyen, A. Diep, K. Hu, A. Iverson, H. Yang, and J.H. Miller Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome DNA Repair (Amst.) 2 2003 593 608
11. P. Hein, and R. Landick The bridge helix coordinates movements of modules in RNA polymerase BMC Biol. 8 2010 141
12. L.M. Heisler, H. Suzuki, R. Landick, and C. Gross Four contiguous amino acids define the target for streptolydigin resistance in the β subunit of Escherichia coli RNA polymerase J. Biol. Chem. 268 1993 25369 25375
13. M. Ho, B. Hudson, K. Das, E. Arnold, and R. Ebright Structures of RNA polymerase-antibiotic complexes Curr. Opin. Struct. Biol. 19 2009 715 723
14. A. Horrevorts, M. Michel, and K. Kerrebijn Antibiotic interaction: interpretation of fractional inhibitory and fractional bactericidal concentration indices Eur. J. Clin. Microbiol. 6 1987 502 503
15. D.J. Jin, and C. Gross Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance J. Mol. Biol. 202 1988 45 58
16. W. Lane, and S. Darst Molecular evolution of multisubunit RNA polymerases: sequence analysis J. Mol. Biol. 395 2010 671 685
17. L. Li, X. Chen, P. Fan, J. Mihalic, and S. Cutler Antibacterial Agents 2001 World Intellectual Property Organization WO/2001/051456
18. L. Li, X. Chen, S. Cutler, and J. Mann Pyrazole Antimicrobial Agents 2001 World Intellectual Property Organization WO/2001/082930
19. N. Lisitsyn, E. Sverdlov, E. Moiseeva, and V. Nikiforov Localization of mutation leading to resistance of E. coli RNA polymerase to the antibiotic streptolydigin in the gene rpoB coding for the β subunit of the enzyme Bioorg. Khim. 11 1985 132 134
20. A. Malinen, M. Nandymazumdar, M. Turtola, H. Malmi, T. Grocholski, I. Artsimovitch, and G. Belogurov CBR antimicrobials alter coupling between the bridge helix and the beta subunit in RNA polymerase Nat. Commun. 5 2014 3408
21. A. McCoy, R. Grosse-Kunstleve, P. Adams, M. Winn, L. Storoni, and R. Read Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
22. J. Meletiadis, S. Pournaras, E. Roilides, and T.J. Walsh Defining fractional inhibitory concentration index cutoffs for additive interactions based on self-drug additive combinations, Monte Carlo simulation analysis, and in vitro-in vivo correlation data for antifungal drug combinations against Aspergillus fumigatus Antimicrob. Agents Chemother. 54 2010 602 609
23. J. Mukhopadhyay, K. Das, S. Ismail, D. Koppstein, M. Jang, B. Hudson, S. Sarafianos, S. Tuske, J. Patel, R. Jansen, and et al. The RNA polymerase "switch region" is a target for inhibitors Cell 135 2008 295 307
24. N. Naryshkin, Y. Kim, Q. Dong, and R. Ebright Site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes Methods Mol. Biol. 148 2001 337 361
25. P. Niyomrattanakit, S.N. Abas, C.C. Lim, D. Beer, P.-Y. Shi, and Y.-L. Chen A fluorescence-based alkaline phosphatase-coupled polymerase assay for identification of inhibitors of dengue virus RNA-dependent RNA polymerase J. Biomol. Screen. 16 2011 201 210
26. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
27. Y. Ovchinnikov, G. Monastyrskaya, V. Gubanov, V. Lipkin, E. Sverdlov, I. Kiver, I. Bass, S. Mindlin, O. Danilevskaya, and R. Khesin Primary structure of Escherichia coli RNA polymerase nucleotide substitution in the β subunit gene of the rifampicin resistant rpoB255 mutant Mol. Gen. Genet. 184 1981 536 538
28. Y. Ovchinnikov, G. Monastyrskaya, S. Guriev, N. Kalinina, E. Sverdlov, A. Gragerov, I. Bass, I. Kiver, E. Moiseyeva, V. Igumnov, and et al. RNA polymerase rifampicin resistance mutations in Escherichia coli: sequence changes and dominance Mol. Gen. Genet. 190 1983 344 348
29. J. Sambrook, and D. Russell Molecular Cloning: A Laboratory Manual 2001 Cold Spring Harbor Laboratory Press
30. K. Severinov, M. Soushko, A. Goldfarb, and V. Nikiforov Rifampicin region revisited: new rifampicin-resistant and streptolydigin-resistant mutants of the β subunit of Escherichia coli RNA polymerase J. Biol. Chem. 268 1993 14820 14825
31. K. Severinov, M. Soushko, A. Goldfarb, and V. Nikiforov RifR mutations in the beginning of the Escherichia coli rpoB gene Mol. Gen. Genet. 244 1994 120 126
32. K. Severinov, D. Markov, E. Severinova, V. Nikiforov, R. Landick, S. Darst, and A. Goldfarb Streptolydigin-resistant mutants in an evolutionarily conserved region of the β' subunit of Escherichia coli RNA polymerase J. Biol. Chem. 270 1995 23926 23929
33. K. Severinov, R. Mooney, S. Darst, and R. Landick Tethering of the large subunits of Escherichia coli RNA polymerase J. Biol. Chem. 272 1997 24137 24140
34. A. Srivastava, M. Talaue, S. Liu, D. Degen, R.Y. Ebright, E. Sineva, A. Chakraborty, S. Druzhinin, S. Chatterjee, J. Mukhopadhyay, and et al. New target for inhibition of bacterial RNA polymerase: "switch region" Curr. Opin. Microbiol. 14 2011 532 543
35. D. Sweetser, M. Nonet, and R. Young Prokaryotic and eukaryotic RNA polymerases have homologous core subunits Proc. Natl. Acad. Sci. USA 84 1987 1192 1196
36. D. Temiakov, N. Zenkin, M. Vassylyeva, A. Perederina, T. Tahirov, K. Kaihatsu, M. Savkina, S. Zorov, V. Nikiforov, N. Igarashi, and et al. Structural basis of transcription inhibition by antibiotic streptolydigin Mol. Cell 19 2005 655 666
37. S. Tuske, S. Sarafianos, X. Wang, B. Hudson, E. Sineva, J. Mukhopadhyay, J. Birktoft, O. Leroy, S. Ismail, A. Clark, and et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation Cell 122 2005 541 552
38. D. Wang, T. Meier, C. Chan, G. Feng, D. Lee, and R. Landick Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex Cell 81 1995 341 350
39. R. Weinzierl The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the bridge helix domain BMC Biol. 8 2010 134
40. R. White, D.S. Burgess, M. Manduru, and J. Bosso Comparison of three different in vitro methods of detecting synergy: time-kill, checkerboard, and E test Antimicrob. Agents Chemother. 40 1996 1914 1918
41. Y. Zhang, D. Degen, M. Ho, E. Sineva, K. Ebright, Y. Ebright, V. Mekler, H. Vahedian-Movahed, Y. Feng, R. Yin, and et al. GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides Elife 3 2014 e02450
42. W. Zhu, J. Haupenthal, M. Groh, M. Fountain, and R. Hartmann New insights into the bacterial RNA polymerase inhibitor CBR703 as a starting point for optimization as an anti-infective agent Antimicrob. Agents Chemother. 58 2014 4242 4245