The Novel Aminomethylcycline Omadacycline Has High Specificity for the Primary Tetracycline-Binding Site on the Bacterial Ribosome.
Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline. All three antibiotics are inhibited by mutations in the 16S rRNA that mediate resistance to tetracycline in Brachyspira hyodysenteriae, Helicobacter pylori, Mycoplasma hominis, and Propionibacterium acnes. Chemical probing with dimethyl sulfate and Fenton cleavage with iron(II)-complexes of the tetracycline derivatives revealed that each antibiotic interacts in an idiosyncratic manner with the ribosome. X-ray crystallography had previously revealed one primary binding site for tetracycline on the ribosome and up to five secondary sites. All tetracyclines analyzed here interact with the primary site and tetracycline also with two secondary sites. In addition, each derivative displays a unique set of non-specific interactions with the 16S rRNA.
Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany. corina.heidrich@gmail.com.
Corina G
CG
Heidrich
Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany. sanya.mitova@hotmail.de.
Sanya
S
Mitova
Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain. aschedlbauer@cicbiogune.es.
Andreas
A
Schedlbauer
Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain. sean.connell@gmail.com.|IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain. sean.connell@gmail.com.
Sean R
SR
Connell
Structural Biology Unit, CIC bioGUNE, 48160 Derio, Bizkaia, Spain. pfucini@gmail.com.|IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain. pfucini@gmail.com.
Paola
P
Fucini
Paratek Pharmaceuticals Inc., King of Prussia, PA 19406, USA. judith.steenbergen@paratekpharma.com.
Judith N
JN
Steenbergen
Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany. christian.berens@fli.de.|Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, 07743 Jena, Germany. christian.berens@fli.de.
Christian
C
Berens
antibiotic resistance; antibiotics; chemical probing; omadacycline; ribosome structure; tetracycline; tetracycline resistance; tigecycline
Methods Enzymol. 2000;317:292-309
10829287
Vet Microbiol. 2007 Jul 20;123(1-3):245-8
17428623
J Biol Chem. 1999 Jun 4;274(23):16576-81
10347223
Antimicrob Agents Chemother. 2014;58(2):1127-35
24295985
Nucleic Acids Res. 2004 May 11;32(8):2594-7
15141029
Antimicrob Agents Chemother. 2006 Jun;50(6):2156-66
16723578
Antimicrob Agents Chemother. 2014;58(3):1707-12
24379204
Biochemistry. 1995 Jan 10;34(1):22-31
7819199
J Inorg Biochem. 1988 Jul;33(3):193-210
3418341
Nucleic Acids Res. 1997 Mar 15;25(6):1219-24
9092632
Ann N Y Acad Sci. 2011 Dec;1241:17-32
22191524
Antimicrob Agents Chemother. 1998 Jul;42(7):1702-5
9661007
Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):1971-6
10051579
J Antimicrob Chemother. 2008 Jun;61(6):1390-2
18356155
J Mol Biol. 2002 Feb 22;316(3):725-68
11866529
Antimicrob Agents Chemother. 2015 Nov;59(11):7044-53
26349824
J Bacteriol. 2002 Apr;184(8):2131-40
11914344
J Bacteriol. 2005 Jun;187(11):3708-12
15901694
J Antimicrob Chemother. 2004 Apr;53(4):592-9
14985271
Clin Microbiol Rev. 2011 Oct;24(4):718-33
21976606
J Mol Biol. 1988 Mar 20;200(2):309-19
3373531
Antimicrob Agents Chemother. 2014;58(1):297-303
24165187
Microbiol Mol Biol Rev. 2001 Jun;65(2):232-60 ; second page, table of contents
11381101
Antimicrob Agents Chemother. 2014;58(3):1279-83
24041885
J Bacteriol. 2002 Sep;184(18):5113-20
12193628
J Biol Inorg Chem. 2008 Sep;13(7):1097-110
18548290
Chem Biol. 1998 Mar;5(3):163-75
9545425
Antimicrob Agents Chemother. 2015 Feb;59(2):796-802
25403668
Antimicrob Agents Chemother. 1999 Apr;43(4):738-44
10103174
Proc Natl Acad Sci U S A. 1984 Jul;81(14):4290-3
6379642
Eur J Biochem. 2002 Jan;269(1):175-83
11784311
Plasmid. 1981 Jul;6(1):112-8
7025054
J Mol Biol. 1986 Feb 5;187(3):399-416
2422386
Cell. 2000 Dec 22;103(7):1143-54
11163189
Antimicrob Agents Chemother. 2007 Jun;51(6):2065-9
17420217
Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3812-6
23431179
Cell Mol Life Sci. 2010 Feb;67(3):419-31
19862477
Nat Struct Mol Biol. 2004 Oct;11(10):1008-14
15448679
Microb Drug Resist. 2000 Winter;6(4):277-82
11272255
J Biol Chem. 1998 Jun 5;273(23):14077-80
9603904
Nature. 1987 Jun 4-10;327(6121):389-94
2953976
Cell. 1986 Dec 26;47(6):985-94
2430725
Biochemistry. 2005 Sep 6;44(35):11829-35
16128584
Antimicrob Agents Chemother. 2012 Nov;56(11):5650-4
22908151
Antimicrob Agents Chemother. 1991 Nov;35(11):2306-11
1725100
EMBO J. 2001 Apr 17;20(8):1829-39
11296217
Int J Antimicrob Agents. 2013 Aug;42(2):133-40
23746717
Antimicrob Agents Chemother. 2015 May;59(5):2849-54
25753625
Nucleic Acids Res. 1994 Sep;22(17):3502-7
7524024