A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Eyal, Zohar ^a   Matzov, Donna ^a   Krupkin, Miri ^a   Paukner, Susanne ^b   Riedl, Rosemarie ^b   Rozenberg, Haim ^a   Zimmerman, Ella ^a   Bashan, Anat ^a   Yonath, Ada ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b Nabriva Therapeutics Inc   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL PROTEIN; DITERPENE; PLEUROMUTILIN;

BACTERIAL 50S RIBOSOMAL SUBUNIT; BIOSYNTHESIS; CHEMISTRY; DRUG EFFECT; GROWTH, DEVELOPMENT AND AGING; HUMAN; METABOLISM; PATHOLOGY; PHASE 3 CLINICAL TRIAL (TOPIC); PROTEIN SYNTHESIS; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS INFECTION;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; CLINICAL TRIALS, PHASE III AS TOPIC; DITERPENES; HUMANS; PROTEIN BIOSYNTHESIS; RIBOSOME SUBUNITS, LARGE, BACTERIAL; STAPHYLOCOCCAL INFECTIONS; STAPHYLOCOCCUS AUREUS;

EID: 85005951102     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep39004     Document Type: Article

References (42)

1. Tong, S. Y., Davis, J. S., Eichenberger, E., Holland, T. L., Fowler, V. G. Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clinical microbiology reviews 28, 603-661 (2015).
2. Kurosu, M., Siricilla, S., Mitachi, K. Advances in MRSA drug discovery: where are we and where do we need to be Expert opinion on drug discovery 8, 1095-1116 (2013).
3. Besier, S., Ludwig, A., Zander, J., Brade, V., Wichelhaus, T. A. Linezolid resistance in Staphylococcus aureus: gene dosage effect, stability, fitness costs, and cross-resistances. Antimicrobial agents and chemotherapy 52, 1570-1572 (2008).
4. Baquero, F. Gram-positive resistance: challenge for the development of new antibiotics. Journal of Antimicrobial Chemotherapy 39, 1-6 (1997).
5. Kavanagh, F., Hervey, A., Robbins, W. J. Antibiotic Substances From Basidiomycetes: VIII. Pleurotus Multilus (Fr. ) Sacc. and Pleurotus Passeckerianus Pilat. Proceedings of the National Academy of Sciences of the United States of America 37, 570 (1951).
6. Hodgin, L. A., HÖGenauer, G. The Mode of Action of Pleuromutilin Derivatives. European Journal of Biochemistry 47, 527-533, doi: 10. 1111/j. 1432-1033. 1974. tb03721. x (1974).
7. HÖGENAUER, G. The mode of action of pleuromutilin derivatives. European journal of Biochemistry 52, 93-98 (1975).
8. Poulsen, S. M., Karlsson, M., Johansson, L. B., Vester, B. The pleuromutilin drugs tiamulin and valnemulin bind to the RNA at the peptidyl transferase centre on the ribosome. Molecular microbiology 41, 1091-1099 (2001).
9. Schlünzen, F., Pyetan, E., Fucini, P., Yonath, A., Harms, J. r. M. Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin. Molecular microbiology 54, 1287-1294 (2004).
10. Davidovich, C. et al. Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity. Proceedings of the National Academy of Sciences 104, 4291-4296 (2007).
11. Gürel, G., Blaha, G., Moore, P. B., Steitz, T. A. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. Journal of molecular biology 389, 146-156 (2009).
12. Eyal, Z. et al. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proceedings of the National Academy of Sciences 112, E5805-E5814 (2015).
13. Long, K. S., Poehlsgaard, J., Kehrenberg, C., Schwarz, S., Vester, B. The Cfr rRNA methyltransferase confers resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A antibiotics. Antimicrobial agents and chemotherapy 50, 2500-2505 (2006).
14. Gentry, D. R., Rittenhouse, S. F., McCloskey, L., Holmes, D. J. Stepwise exposure of Staphylococcus aureus to pleuromutilins is associated with stepwise acquisition of mutations in rplC and minimally affects susceptibility to retapamulin. Antimicrobial agents and chemotherapy 51, 2048-2052 (2007).
15. Paukner, S., Clark, C., Ivezic-Schoenfeld, Z., Kosowska-Shick, K. Single-and Multistep Resistance Selection with the Pleuromutilin Antibiotic BC-3781. Fifty-second Interscience Conference on Antimicrobial Agents and Chemotherapy, San Francisco, CA. Poster C1-1971 (2012).
16. Paukner, S., Sader, H. S., Ivezic-Schoenfeld, Z., Jones, R. N. Antimicrobial activity of the pleuromutilin antibiotic BC-3781 against bacterial pathogens isolated in the SENTRY Antimicrobial Surveillance Program (2010). Antimicrobial agents and chemotherapy AAC. 00358-00313 (2013).
17. Prince, W. et al. A Phase II clinical study of BC-3781, a pleuromutilin antibiotic, in the treatment of patients with acute bacterial skin and skin structure infection. Antimicrobial agents and chemotherapy AAC. 02106-02112 (2013).
18. François, B. et al. Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic acids research 33, 5677-5690 (2005).
19. Kondo, J., Koganei, M., Kasahara, T. Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site. ACS medicinal chemistry letters 3, 741-744 (2012).
20. Paukner, S., Strickmann, D. B., Ivezic-Schoenfeld, Z. Extended Spectrum Pleuromutilins: Mode-of-Action Studies 24th ECCMID (European Congress of Clinical Microbiology and Infectious Diseases), Barcelona, Spain (2014).
21. Ben-Shem, A. et al. The structure of the eukaryotic ribosome at 3. 0resolution. Science 334, 1524-1529 (2011).
22. Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., Ban, N. Atomic structures of the eukaryotic ribosome. Trends in biochemical sciences 37, 189-198 (2012).
23. Shalev-Benami, M. et al. 2. 8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania. Cell Reports (2016).
24. Khatter, H., Myasnikov, A. G., Natchiar, S. K., Klaholz, B. P. Structure of the human 80S ribosome. Nature 520, 640-645 (2015).
25. de Loubresse, N. G. et al. Structural basis for the inhibition of the eukaryotic ribosome. Nature 513, 517-522 (2014).
26. Dirheimer, G., K., G., Dumas, P., Westhof, E. tRNA: Structure, Biosynthesis, and Function (Söll, D., RajBhandary, U. Eds). (American Society for Microbiology, Washington, 1995).
27. Wilson, D. N. On the specificity of antibiotics targeting the large ribosomal subunit. Annals of the New York Academy of Sciences 1241, 1-16 (2011).
28. Novick, R. P. [27] Genetic systems in Staphylococci. Methods in enzymology 204, 587-636 (1991).
29. Otwinowski, Z., Minor, W. Processing of X-ray diffraction data. Methods enzymol 276, 307-326 (1997).
30. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallographica Section D: Biological Crystallography 67, 235-242 (2011).
31. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221 (2010).
32. Emsley, P., Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 (2004).
33. Emsley, P., Lohkamp, B., Scott, W. G., Cowtan, K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66, 486-501 (2010).
34. Chou, F.-C., Sripakdeevong, P., Dibrov, S. M., Hermann, T., Das, R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nature methods 10, 74-76 (2012).
35. Schrodinger, L. L. C. The PyMOL Molecular Graphics System, Version 1. 3r1 (2010).
36. Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. Journal of computational chemistry 25, 1605-1612 (2004).
37. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. Basic local alignment search tool. J Mol Biol 215, 403-410 (1990).
38. Kleywegt, G. J., Jones, T. A. Where freedom is given, liberties are taken. Structure 3, 535-540 (1995).
39. Katoh, K., Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution 30, 772-780 (2013).
40. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., Barton, G. J. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189-1191 (2009).
41. Murray, R. W., Melchior, E. P., Hagadorn, J. C., Marotti, K. R. Staphylococcus aureus cell extract transcription-translation assay: firefly luciferase reporter system for evaluating protein translation inhibitors. Antimicrobial agents and chemotherapy 45, 1900-1904 (2001).
42. Leatherbarrow, R. J. GraFit Version 7, Erithacus Software Ltd. Horley, U. K. (2009).