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Chapter 17 : Inhibitors of the 30S Ribosomal Subunit

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Abstract:

The aminoglycoside group of antibiotics are multifunctional hydrophilic carbohydrates that possess two or more amino monosaccharides connected by glycosidic bonds to an aminocyclitol nucleus. Most aminoglycosides contain a 2-deoxystreptamine cyclitol. The aminoglycoside antibiotics have several features justifying their continued clinical use, including their rapid and potent bactericidal activity, long-lasting postantibiotic effect, and synergy with other antibiotics. The emerging structural data now have the potential to be exploited in the design of specific inhibitors of enzyme activity. The challenge is to use this information to synthesize effective and potent inhibitors that will overcome antibiotic resistance produced by the aminoglycoside-modifying enzymes. The tetracyclines are a group of antibiotics with an identical basic skeleton of four linearly fused six-membered rings, named 1,4,4a,5,5a,6,11,12-octahydronaphthacene and differing from each other chemically only by substituent variation at positions 5, 6, and 7. It has been found that there are two binding sites for tetracycline within the small ribosomal subunit. Bacterial resistance results from the selective pressure exerted on bacteria during the administration of tetracyclines for chemotherapy. Resistance to tetracycline may be mediated by one of three different mechanisms: (i) an energy-dependent efflux of tetracyclines carried out by transmembrane spanning proteins, which results in reduction of the concentration of tetracycline in the cytosol; (ii) ribosomal protection, whereby the tetracyclines no longer bind productively to the bacterial ribosome; or (iii) chemical modification, requiring oxygen and NADPH and catalysis by enzymes. Since the chemical alteration mechanism occurs rarely, this discussion focuses on the major mechanisms of tetracycline resistance.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Figures

Image of Figure 17.1
Figure 17.1

Classification of aminoglycoside antibiotics based on the chemical structure of the aminocyclitol: streptidine, streptamine, or 2-deoxystreptamine, including those in which the amino sugars are linked at the 4- and 5-hydroxyl groups and those substituted at the 4- and 6-hydroxyl positions.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.2
Figure 17.2

Chemical structures of streptomycin and dihydrostreptomycin.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.3
Figure 17.3

Chemical structure of spectinomycin chlorhydrate drawn conformationally and planar. At the right is the 3-keto form, which is hydrated in aqueous medium, forming a diol group as shown.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.4
Figure 17.4

Chemical structures of neomycin B, paromomycin, and ribostamycin, with the atomic and ring-numbering systems denoted in arabic and roman numerals, respectively.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.5
Figure 17.5

Chemical structures of kanamycins A, B, and C, amikacin, dibekacin, and tobramycin.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.6
Figure 17.6

Chemical structures of gentamicins C1, C2, and C1a.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.7
Figure 17.7

Chemical structures of sisomicin and netilmicin.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.8
Figure 17.8

Secondary structure of E. coli 16S rRNA . This four-domain structure is 46% base paired, highlighting the decoding region A site. Nucleotides conserved in more than 95% of ribosomal sequences are shown in outline. Adapted from M. O'Connor, M. Bayfield, S. T. Gregory, W.-C. M. Lee, J. S. Lodmell, A. Mankad, J. R. Thompson, A. Vila-Sanjurjo, C. L. Squires, and A. E. Dahlberg, p. 217–227, in R. A. Garrett, S. R. Douthwaite, A. Liljas, A. T. Matheson, P. B. Moore, and H. F. Noller (ed.), The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (ASM Press, Washington, D.C., 2000), with permission from the publisher.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.9
Figure 17.9

Secondary structure of the 27-mer A-site RNA oligonucleotide, as derived by NMR. Watson-Crick base pairs are denoted by solid lines, while mismatched base pairs are denoted by dashed lines. Bases present in E. coli 16S rRNA are depicted in bold type and are numbered as in 16S rRNA. The aminoglycoside-binding site, as revealed by NMR and footprinting studies, is as indicated. Reprinted from M. Kaul and D. S. Pilch, Biochemistry 41:7695–7706, 2002, with permission from the publisher.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.10
Figure 17.10

The streptomycin-binding site. For details, see the text. Adapted from A. P. Carter, W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan, Nature 407:340–348, 2000, with permission from the publisher.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.11
Figure 17.11

Enzymatic inactivation of kanamycin B. Not all resistant bacteria exhibit every reaction shown.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.12
Figure 17.12

Chemical structure of isepamicin compared to that of amikacin.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.13
Figure 17.13

Chemical structure of arbekacin.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.14
Figure 17.14

Chemical structures of seven clinically important tetracyclines (for an explanation, see the text).

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.15
Figure 17.15

Chemical structure of tetracycline hydrochloride.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.16
Figure 17.16

Chemical instability of tetracycline under acidic and basic conditions. Note that the 6β-hydroxy group participates in these degradation reactions.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.17
Figure 17.17

Epimerization of the tetracycline subsituents at C-4 in acidic medium (pH 2 to 6).

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.18
Figure 17.18

Diagrammatic representation of tetracycline accumulation in sensitive (top) and resistant (bottom) bacterial cells. Sensitive cells show a net active uptake, while resistant cells show a net active efflux. T, tetracycline. Reprinted from L. E. Bryan (ed.), Antimicrobial Drug Resistance (Academic Press, Inc., New York, N.Y., 1984), with permission from the publisher.

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Image of Figure 17.19
Figure 17.19

Chemical structure of N,N-dimethylglycylamido derivatives of 9- aminominocycline (DMG-MINO) and 9-amino-6-demethyl-6-deoxytetracycline (DMGDMDOT).

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
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Tables

Generic image for table
Table 17.1

Typical enzymes modifying clinically used aminoglycosides

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
Generic image for table
Table 17.2

Generic and common trade names of aminoglycosides, the preparations available, and manufacturers in the United States

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
Generic image for table
Table 17.3

Classification of tetracycline resistance determinants according to their mechanism of resistance a

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17
Generic image for table
Table 17.4

List of generic and common trade names of tetracyclines, the preparations available, and manufacturers in the United States

Citation: Mascaretti O. 2003. Inhibitors of the 30S Ribosomal Subunit, p 229-246. In Bacteria versus Antibacterial Agents. ASM Press, Washington, DC. doi: 10.1128/9781555817794.ch17

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