Bacterial Transcription Inhibitor of RNA Polymerase Holoenzyme Formation by Structure-Based Drug Design: From in Silico Screening to Validation

ACS Infectious Diseases

Volumn 2, Issue 1, 2016, Pages 39-46

  Ma, Cong ^a   Yang, Xiao ^a   Lewis, Peter J ^a  

^a UNIVERSITY OF NEWCASTLE   (Australia)

Author keywords

antibiotic discovery; bacteria; in silico screening; protein protein interaction; target validation; transcription

Indexed keywords

ANTIINFECTIVE AGENT; ENZYME INHIBITOR; DNA DIRECTED RNA POLYMERASE; HOLOENZYME; PROTEIN BINDING;

ANTIBACTERIAL ACTIVITY; ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; DRUG DESIGN; DRUG SCREENING; ENZYME LINKED IMMUNOSORBENT ASSAY; ESCHERICHIA COLI; FAR WESTERN BLOTTING; GROWTH INHIBITION; ISOTHERMAL TITRATION CALORIMETRY; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MICROSCOPY; NONHUMAN; PHARMACOPHORE; PHOTON CORRELATION SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; BIOLOGY; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; METABOLISM; MICROBIAL SENSITIVITY TEST; REPRODUCIBILITY; STRUCTURAL HOMOLOGY; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION INITIATION; TRENDS; VALIDATION STUDY;

ANTI-BACTERIAL AGENTS; BACILLUS SUBTILIS; COMPUTATIONAL BIOLOGY; DNA-DIRECTED RNA POLYMERASES; DRUG DESIGN; GENE EXPRESSION REGULATION, BACTERIAL; HOLOENZYMES; HUMANS; MICROBIAL SENSITIVITY TESTS; PROTEIN BINDING; REPRODUCIBILITY OF RESULTS; STRUCTURAL HOMOLOGY, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ACTIVATION;

EID: 84969136103     PISSN: None     EISSN: 23738227     Source Type: Journal    
DOI: 10.1021/acsinfecdis.5b00058     Document Type: Article

References (30)

1. WHO. ((2014) Antimicrobial Resistance: Global Report on Surveilance 2014, pp 1-257, Geneva, Switzerland.
2. O'Neill, J. (2014) Review on Antimicrobial Resistance: Tackling a Crisis for the Health and Wealth of Nations, HMSO, London, UK.
3. Cramer, P. (2002) Multisubunit RNA polymerases Curr. Opin. Struct. Biol. 12 (1) 89-97 10.1016/S0959-440X(02)00294-4
4. Sensi, P., Margalith, P., and Timbal, M. T. (1959) Rifomycin, a new antibiotic; preliminary report Farmaco Sci. 14 (2) 146-147
5. Scott, L. J. (2013) Fidaxomicin: a review of its use in patients with Clostridium difficile infection Drugs 73 (15) 1733-1747 10.1007/s40265-013-0134-z
6. Mariani, R. and Maffioli, S. I. (2009) Bacterial RNA polymerase inhibitors: an organized overview of their structure, derivatives, biological activity and current clinical development status Curr. Med. Chem. 16 (4) 430-454 10.2174/092986709787315559
7. Villain-Guillot, P. et al. 2007, Progress in targeting bacterial transcription Drug Discovery Today 12 (5-6) 200-208 10.1016/j.drudis.2007.01.005
8. Sonenshein, A. L. et al. 1977, Lipiarmycin-resistant ribonucleic acid polymerase mutants of Bacillus subtilis J. Bacteriol. 132 (1) 73-79
9. Keller, A. et al. 2014, A new subunit of RNA polymerase found in Gram positive bacteria J. Bacteriol. 196, 3622-3632 10.1128/JB.02020-14
10. Murakami, K. S. and Darst, S. A. (2003) Bacterial RNA polymerases: the whole story Curr. Opin. Struct. Biol. 13 (1) 31-39 10.1016/S0959-440X(02)00005-2
11. Andre, E. et al. 2004, A multiwell assay to isolate compounds inhibiting the assembly of the prokaryotic RNA polymerase Assay Drug Dev. Technol. 2 (6) 629-635 10.1089/adt.2004.2.629
12. Hinsberger, S. et al. 2013, Discovery of novel bacterial RNA polymerase inhibitors: pharmacophore-based virtual screening and hit optimization J. Med. Chem. 56 (21) 8332-8338 10.1021/jm400485e
13. Arthur, T. M., Anthony, L. C., and Burgess, R. R. (2000) Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase J. Biol. Chem. 275 (30) 23113-23119 10.1074/jbc.M002040200
14. Ma, C. et al. 2013, Inhibitors of bacterial transcription initiation complex formation ACS Chem. Biol. 8 (9) 1972-1980 10.1021/cb400231p
15. Johnston, E. B., Lewis, P. J., and Griffith, R. (2009) The interaction of Bacillus subtilis sigmaA with RNA polymerase Protein Sci. 18 (11) 2287-2297 10.1002/pro.239
16. Bergendahl, V., Heyduk, T., and Burgess, R. R. (2003) Luminescence resonance energy transfer-based high-throughput screening assay for inhibitors of essential protein-protein interactions in bacterial RNA polymerase Appl. Environ. Microbiol. 69 (3) 1492-1498 10.1128/AEM.69.3.1492-1498.2003
17. Glaser, B. T. et al. 2007, LRET-based HTS of a small-compound library for inhibitors of bacterial RNA polymerase Assay Drug Dev. Technol. 5 (6) 759-768 10.1089/adt.2007.095
18. Lipinski, C. A. et al. 2001, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 46 (1-3) 3-26 10.1016/S0169-409X(00)00129-0
19. Kostrewa, D. et al. 2009, RNA polymerase II-TFIIB structure and mechanism of transcription initiation Nature 462 (7271) 323-330 10.1038/nature08548
20. Mooney, R. A. et al. 2009, Regulator trafficking on bacterial transcription units in vivo Mol. Cell 33 (1) 97-108 10.1016/j.molcel.2008.12.021
21. Johnson, A. S., van Horck, S., and Lewis, P. J. (2004) Dynamic localization of membrane proteins in Bacillus subtilis Microbiology 150 (Pt 9) 2815-2824 10.1099/mic.0.27223-0
22. Lewis, P. J., Thaker, S. D., and Errington, J. (2000) Compartmentalization of transcription and translation in Bacillus subtilis EMBO J. 19 (4) 710-718 10.1093/emboj/19.4.710
23. Dworsky, P. (1975) Unfolding of the chromosome of Escherichia coli after treatment with rifampicin Z. Allg. Mikrobiol. 15 (4) 243-247 10.1002/jobm.3630150404
24. Davies, J. and Davies, D. (2010) Origins and evolution of antibiotic resistance Microbiol. Mol. Biol. Rev. 74 (3) 417-433 10.1128/MMBR.00016-10
25. Yang, X. and Lewis, P. J. (2008) Overproduction and purification of recombinant Bacillus subtilis RNA polymerase Protein Expression Purif. 59 (1) 86-93 10.1016/j.pep.2008.01.006
26. Yang, X., Ma, C., and Lewis, P. J. (2015) Identification of inhibitors of bacterial RNA polymerase Methods 86, 45-50 10.1016/j.ymeth.2015.05.005
27. Artsimovitch, I. and Henkin, T. M. (2009) In vitro approaches to analysis of transcription termination Methods 47 (1) 37-43 10.1016/j.ymeth.2008.10.006
28. Doherty, G. P. et al. 2010, Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition Microbiology 156 (Pt 12) 3532-3543 10.1099/mic.0.041566-0
29. Studier, F. W. and Moffatt, B. A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes J. Mol. Biol. 189 (1) 113-130 10.1016/0022-2836(86)90385-2
30. Buescher, J. M. et al. 2012, Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism Science 335 (6072) 1099-1103 10.1126/science.1206871