Inhibitors of the Elongation Cycle of Protein Synthesis

Abstract

The protein synthetic machinery is a highly complex apparatus that offers many potential sites for functional interference and represents a major target in the cell for antibiotics. The knowledge of ribosomal structure and function has progressed enormously in recent years, which has, in turn, accelerated our understanding of the mechanism of drug action. Conversely, drugs have been used as tools to probe the translation cycle, thus providing a means to further dissect the multitude of steps involved in protein synthesis. In an era where bacteria are showing an ever‐increasing resistance to many clinically relevant antibiotics, the importance of understanding their mechanism of inhibition is essential to the development of novel and more effective replacements.

Key concept:

  • A large number of antibiotics target the ribosome and inhibit specific steps during the elongation cycle.

Keywords: antibiotics; ribosomes; RNA; antibiotic resistance

Figure 1.

Inhibition of the initiation and elongation phases of translation by antibiotics. The antibiotics discussed in this article are highlighted in red. This figure was updated and modified from Spahn and Presscott .

Figure 2.

Regions of the small and large rRNA associated with various antibiotics. Residues associated with known antibiotic‐binding sites are represented on the (a) small and (b) large ribosomal subunit crystal structures using red spacefill. For the 30S, the ribosomal proteins are shown (dark blue) and h44 is highlighted in yellow as a reference, whereas on the 50S only the 23S rRNA is shown, with two regions that are targeted by antibiotics; the PTC/tunnel region (centre) and region associated with factor binding and GTPase activation (right).

Figure 3.

The primary and secondary Tet‐binding sites on the 30S subunit. (a) Overview of the primary and secondary Tet‐binding sites (pdb 1hnw) (Brodersen et al., ), with h34 (blue), H31 (dark green), h18 (light green) and h44 (yellow) highlighted. (b) The chemical structure of Tet, with polar face and rings A–D indicated. (c) In the primary binding site, the charged or polar face of Tet makes contact exclusively with the phosphate backbone of the 16S rRNA (positions G1053, C1054, 1195–1198 of h34 (blue) and 966 of h31 (green); note that position A965 and the base of U1196 are omitted for clarity) except for stacking interaction with the base of G1054.

Figure 4.

The streptomycin‐binding site on the 30S subunit. (a) Overview of Str‐binding site (pdb 1FJG) (Carter et al., ) with Str in red spacefill. The 16S rRNA is in ribbons with h1 (cyan), 530 loop or h18 (green), h27 (yellow), h28 (magenta) and h44 (dark blue) and ribosomal protein S12 (dark green) illustrated. (b) Detailed view of the Str‐binding site. Str (red) interacts exclusively with sugar‐phosphate backbone of the 16S rRNA and in doing so locks together all four of the 16S rRNA domains, namely, the 5′ domain (U14 in h1), the central domain (G526 and C527 in the 530 loop), 3′ major domain (A913 and A914 in h27/h28) and 3′ minor domain (C1490 and G1491 of h44). Lysine 45 of S12 interacts with ring I of Str and also the phosphate oxygen of A913. All colours are as in (a). (c) Chemical structure of Str with rings I–III indicated.

Figure 5.

Overview of the aminoglycoside Par‐binding site on the T. thermophilus 30S subunit (pdb 1ibk). (a) Ribbons representation of 16S rRNA (light blue) and ribosomal proteins (dark blue) with h44 highlighted in yellow and the flipped out A1492 and A1493 in green. Par is shown in red spacefill representation bound at the top of h44. (b) Close‐up view of Par‐binding site within h44. The flipped out bases of A1492 and A1493 (green), the G1491–C1409 base pair that forms the shelf on which ring I sits (pale blue and pink, respectively) as well as U1405 (yellow) and G1494, U1495 and G1496 (orange) are coloured. Hydrogen bond interactions are indicated with a dashed line, for example, in the Watson–Crick 1405–1496 base pair. Par is coloured red. (c) The structure of Par with rings I–IV labelled and the 4‐ and 5‐DOS substituted positions marked in red.

Figure 6.

Puro binds at the peptidyltransferase centre of the 50S subunit. (a) Comparison of structures of Puro with the terminal adenine (A76) aminoacylated with phenylalanine. Differences between Puro and the physiological tRNA substrate are indicated in red on the tRNA. Puro bound to the H. marismortui 50S ribosomal subunit in the form of (b) the Yarus inhibitor (pdb 1FFZ; Nissen et al., ) and (c) the products following peptide bond formation (pdb 1KQS; Schmeing et al., ). The Puro part in each of the respective compounds is coloured red. Selected rRNA residues of domain V of the 23S rRNA are coloured light blue, including the A‐ and P‐loop bases that participate in A and P sites CCA‐end fixation (E. coli numbering). In (b) the A site C74 and C75 mimics have been omitted for clarity, likewise in (c) for the P site product. Dashes indicate hydrogen bonding and rRNA nucleotides use the following colour scheme: oxygen, red; phosphorus, yellow; nitrogen, blue and carbon, dark blue.

Figure 7.

Macrolides bind within the tunnel of the 50S subunit. View from the base of the 50S subunit looking up the tunnel towards the PTC in the absence (a) and presence (b) of the macrolide carbomycin (red spacefill in (b)). The rRNA (pink) and ribosomal proteins (magenta) are in ribbons, with ribosomal protein L4 (blue) and L22 (green), whose long extensions reach into the tunnel of the 50S subunit, are highlighted. (c) The C5 side chain of carbomycin (red) reaches into the PTC and approaches A2451 (very close to the site of peptide bond formation as seen in Figure a). Also indicated are 23S rRNA residues A2062 (green), the N6 of which forms a covalent bond with the acetaldehyde group at the C6 position of the lactone ring of carbomycin, and G2058 (yellow), the N2 of which is in van der Waals distance with the C4 and C7 positions of the lactone ring preventing hydrogen bond formation with the mycaminose C5 sugar position. (d) Comparison of chemical structures of carbomycin A and erythromycin, illustrating the sugar side chains at the C3 and C5 positions and the aldehyde of carbomycin at the C6 position.

Figure 8.

The thiostrepton‐binding site on the 50S subunit. (a) Overview of the L11‐binding site on the D. radiodurans 50S subunit, with boxed region enlarged to show insertion of thiostrepton into cleft between L11‐NTD (yellow) and 23S rRNA helices 43 and 44 (H43/44; orange) (Harms et al., ). (b) The thiazole rings (THZ) of thiostrepton (Thio, green) stack on proline residues (P22, P26) in the L11‐NTD (yellow) and interact with the bases A1067 and A1095 at the tips of H43/44 (orange). (c) Cryo‐EM map (grey) of EF‐G bound to the 70S ribosome, with crystal structures of EF‐G (green) and L11 (yellow, orange) and L7 (purple) region docked. (d) Superimposition of the position of thiostrepton (Thio, cyan) with domain V of EF‐G (green) as well as comparison of position of L11‐NTD in the EF‐G‐70S cryo‐EM map (EF‐G‐L11, yellow) (Connell et al., ) and the D. radiodurans 50S‐thiostrepton crystal structure (Thio‐L11, cyan) (Harms et al., ).

Figure 9.

Spectinomycin‐binding site on the 30S subunit. (a) Overview of the Spt‐binding site on the 30S subunit (pdb 1fjg; Carter et al., ). Ribbons representation of 16S rRNA (light blue) with h34 (purple), h30/35 (yellow), h38 (green) and h28 (cyan) is highlighted, in addition to ribosomal protein S5 (dark blue). (b) Close‐up view of the Spt‐binding site at the elbow junction of h34 and h30, where hydrogen bond interactions (dashed blue line) between Spt (red) and G1068 (h30) and C1066, G1064 and C1192 (counter clockwise) are shown. Other colours are as in (a). (c) Chemical structure of Spt.

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Further Reading

Gaynor M and Mankin A (2003) Macrolide antibiotics: binding site, mechanisms of action, resistence. Current Topics in Medicinal Chemistry 3: 949–961.

Moore P and Steitz T (2003) The structural basis of large ribosomal submit function. Annual Review of Biochemistry 72: 813–850.

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Ramakrishnan V (2002) Ribosome structure and the mechanism of translation. Cell 108: 557–572.

Wilson DN (2004) Antibiotics and the inhibition of ribosome function. In: Nierhaus KH and Wilson DN (eds) Protein Synthesis and Ribosome Structure, pp. 449–527. Weinheim: Wiley‐VCH.

Wilson DN and Nierhaus KH (2003) The ribosome through the looking glass. Angewandte Chemistry International Edition 42: 3464–3486.

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Wilson, Daniel N, Starosta, Agata L, Yamamoto, Hiroshi, and Nierhaus, Knud H(Sep 2009) Inhibitors of the Elongation Cycle of Protein Synthesis. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000550.pub2]