ACS Chemical Biology
Articles
tion refinements and B-factor refinements. The statistics of structure
refinement are summarized in Supporting Information Table S3.
Molecular drawings were made using PyMOL.
(11) Howells, J. D., Anderson, L. E., Coffey, G. L., Senos, G. D.,
Underhill, M. A., Vogler, D. L., and Ehrlich, J. (1972) Butirosin, a new
aminoglycosidic antibiotic complex: Bacterial origin and some
microbiological studies. Antimicrob. Agents Chemother. 2, 79−83.
(12) Price, K. E. (1986) Aminoglycoside research 1975−1985:
Prospects for development of improved agents. Antimicrob. Agents
Chemother. 29, 543−548.
(13) Shaw, K. J., Rather, P. N., Hare, R. S., and Miller, G. H. (1993)
Molecular genetics of aminoglycoside resistance genes and familial
relationships of the aminoglycoside-modifying enzymes. Microbiol. Rev.
57, 138−163.
(14) Mingeot-Leclercq, M. P., Glupczynski, Y., and Tulkens, P. M.
(1999) Aminoglycosides: Activity and resistance. Antimicrob. Agents
Chemother. 43, 727−737.
(15) Azucena, E., and Mobashery, S. (2001) Aminoglycoside-
modifying enzymes: Mechanisms of catalytic processes and inhibition.
Drug Resist. Updates 4, 106−117.
ASSOCIATED CONTENT
* Supporting Information
■
S
Figures S1−S8, Tables S1−S3, experimental procedures, X-ray
coordinate files, full spectroscopic data, GC and HPLC reports.
This material is available free of charge via the Internet at
Accession Codes
The atomic coordinates for the A-site•18 complex have been
deposited in the Protein Data Bank (PDB) with the ID code
3WRU.
AUTHOR INFORMATION
Corresponding Author
■
(16) Magnet, S., and Blanchard, J. S. (2005) Molecular insights into
aminoglycoside action and resistance. Chem. Rev. 105, 477−498.
(17) Paulsen, I. T., Brown, M. H., and Skurray, R. A. (1996) Proton-
dependent multidrug efflux systems. Microbiol. Rev. 60, 575−608.
(18) Kondo, J., Pachamuthu, K., Francois, B., Szychowski, J.,
Hanessian, S., and Westhof, E. (2007) Crystal structure of the
bacterial ribosomal decoding site complexed with a synthetic doubly
functionalized paromomycin derivative: A new specific binding mode
to an A-minor motif enhances in vitro antibacterial activity.
ChemMedChem 2, 1631−1638.
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This work was supported by the Achaogen Research Chair and
the Natural Sciences and Engineering Research Council of
Canada (NSERC). J.P.M. received fellowship support from
(19) Hanessian, S., Pachamuthu, K., Szychowski, J., Giguer
Swayze, E. E., Migawa, M. T., Francois, B., Kondo, J., and Westhof, E.
(2010) Bioorg. Med. Chem. Lett. 20, 7097−7101.
(20) Hanessian, S., Giguere, A., Grzyb, J., Maianti, J. P., Saavedra, O.
̀
e, A.,
́ ́
Fonds de Recherche en Sante du Quebec (FRSQ). J.K. was
̧
supported by a Grant-in-Aid for Young Scientists (23790054)
from the Ministry of Education, Culture, Sports, Science and
Technology, Japan. We acknowledge the Photon Factory
synchrotron radiation facilities (No. 2012G519) and the BL-
̀
M., Aggen, J. B., Linsell, M. S., Goldblum, A. A., Hildebrandt, D. J.,
Kane, T. R., Dozzo, P., Gliedt, M. J., Matias, R. D., Feeney, L. A., and
Armstrong, E. S. (2011) Toward overcoming Staphylococcus aureus
aminoglycoside resistance mechanisms with a functionally designed
neomycin analogue. ACS Med. Chem. Lett. 2, 924−928.
̂
5A beamline staff. We thank Dr. Deschenes-Simard for X-ray
structure analysis of 12 and ent-12.
(21) Hanessian, S., Maianti, J. P., Matias, R. D., Feeney, L. A., and
Armstrong, E. S. (2011) Hybrid aminoglycoside antibiotics via Tsuji
palladium-catalyzed allylic deoxygenation. Org. Lett. 13, 6476−6479.
(22) Kahlmeter, G., and Dahlager, J. I. (1984) Aminoglycoside
toxicityA review of clinical studies published between 1975 and
1982. J. Antimicrob. Chemother. 13 (Suppl A), 9−22.
(23) Chen, L., Hainrichson, M., Bourdetsky, D., Mor, A., Yaron, S.,
and Baasov, T. (2008) Structure-toxicity relationship of aminoglyco-
sides: correlation of 2′-amine basicity with acute toxicity in pseudo-
disaccharide scaffolds. Bioorg. Med. Chem. 16, 8940−8951.
(24) Mingeot-Leclercq, M. P., and Tulkens, P. M. (1999)
Aminoglycosides: nephrotoxicity. Antimicrob. Agents Chemother. 43,
1003−1012.
(25) Nudelman, I., Rebibo-Sabbah, A., Cherniavsky, M., Belakhov, V.,
Hainrichson, M., Chen, F., Schacht, J., Pilch, D. S., Ben-Yosef, T., and
Baasov, T. (2009) Development of novel aminoglycoside (NB54) with
reduced toxicity and enhanced suppression of disease-causing
premature stop mutations. J. Med. Chem. 52, 2836−2845.
(26) Kondo, J. (2012) A structural basis for the antibiotic resistance
conferred by an A1408G mutation in 16S rRNA and for the
antiprotozoal activity of aminoglycosides. Angew. Chem., Int. Ed. Engl.
51, 465−468.
(27) Kondo, J., Koganei, M., Maianti, J. P., Ly, V. L., and Hanessian,
S. (2013) Crystal structures of a bioactive 6′-hydroxy variant of
sisomicin bound to the bacterial and protozoal ribosomal decoding
sites. ChemMedChem 8, 733−739.
REFERENCES
■
(1) Arya, D. P. (2007) Aminoglycoside Antibiotics: From Chemical
Biology to Drug Discovery, Wiley-Interscience, Hoboken, NJ.
(2) Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren,
R. J., Wimberly, B. T., and Ramakrishnan, V. (2000) Functional
insights from the structure of the 30S ribosomal subunit and its
interactions with antibiotics. Nature 407, 340−348.
(3) Wimberly, B. T., Brodersen, D. E., Clemons, W. M., Jr., Morgan-
Warren, R. J., Carter, A. P., Vonrhein, C., Hartsch, T., and
Ramakrishnan, V. (2000) Structure of the 30S ribosomal subunit.
Nature 407, 327−339.
(4) Ogle, J. M., and Ramakrishnan, V. (2005) Structural insights into
translational fidelity. Annu. Rev. Biochem. 74, 129−177.
(5) Francois, B., Russell, R. J., Murray, J. B., Aboul-ela, F., Masquida,
B., Vicens, Q., and Westhof, E. (2005) 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 Res. 33, 5677−5690.
(6) Wilson, D. N. (2009) The A−Z of bacterial translation inhibitors.
Crit. Rev. Biochem. Mol. Biol. 44, 393−433.
(7) Kohanski, M. A., Dwyer, D. J., and Collins, J. J. (2010) How
antibiotics kill bacteria: From targets to networks. Nat. Rev. Microbiol.
8, 423−435.
(8) Boucher, H. W., Talbot, G. H., Bradley, J. S., Edwards, J. E.,
Gilbert, D., Rice, L. B., Scheld, M., Spellberg, B., and Bartlett, J. (2009)
Bad bugs, no drugs: no ESKAPE! An update from the Infectious
Diseases Society of America. Clin. Infect. Dis. 48, 1−12.
(9) Waksman, S. A., Lechevalier, H. A., and Harris, D. A. (1949)
Neomycin: Production and antibiotic properties. J. Clin. Invest. 28,
934−939.
(28) Perez-Fernandez, D., Shcherbakov, D., Matt, T., Leong, N. C.,
Kudyba, I., Duscha, S., Boukari, H., Patak, R., Dubbaka, S. R., Lang, K.,
Meyer, M., Akbergenov, R., Freihofer, P., Vaddi, S., Thommes, P.,
Ramakrishnan, V., Vasella, A., and Bottger, E. C. (2014) 4′-O-
substitutions determine selectivity of aminoglycoside antibiotics. Nat.
Commun. 5, 3112.
(10) Davidson, R. N., den Boer, M., and Ritmeijer, K. (2009)
Paromomycin. Trans. R. Soc. Trop. Med. Hyg. 103, 653−660.
2072
dx.doi.org/10.1021/cb5003416 | ACS Chem. Biol. 2014, 9, 2067−2073