Macrolides

● Types

Discovery

The first macrolide antibiotic, called pikromycin, was isolated from a Streptomyces strain in 1950 (Dinos, 2017). In 1952, the 14-membered macrolide, Erythromycin, was used to treat a bacterial infection at Minneapolis General Hospital (Amdan et al., 2024). Over the years many derivatives of this molecule (e.g., azithromycin and clarithromycin) have been developed to improve its stability in an acidic environment (stomach) and increase its bioavailability.

Macrolides bind to bacterial 50S ribosomal subunit and interfere with protein synthesis. They have a broad spectrum of activity - mainly effective against gram-positive bacteria such as Staphylococcus spp., Streptococcus spp., and Diplococcus spp., and only limited activity against gram-negative bacteria such as Neisseria gonorrhoeae, Haemophilus influenzae, and Bordetella pertussis. Note that some macrolides are active against various Mycoplasmas, but this class of molecules has a low affinity for eukaryotic ribosomes, so it can be used as antimicrobials.

Overview of Chemistry

Macrolides are a class of hydrophobic antibiotics characterized by their macrocyclic lactone ring (with 12-16 atoms) (Amdan et al., 2024). Larger (17-18 atom) ring macrolides are also known to have antibiotic activity but they inhibit RNA polymerase function (Golkar et al., 2018).

They are synthesized naturally by polyketide-synthases present in various Streptomyces sp. and then glycosylated with one or more deoxy‐ or amino sugars. The lactone rings possess a hydrophobic and a hydrophilic face, and they invariably bind to the ribosome with their hydrophobic face. Glycosylations in macrolides introduce diverse chemical properties in this class of molecules (Golkar et al., 2018). The hexose sugar linked at the macrolactone's C5 position is usually a desosamine (shown in Figure 1) or a mycaminose. If the latter sugar is present, a second sugar is frequently attached, creating a disaccharide at the C5 position. A cladinose (sugar) is frequently linked to the C3 position of the ring.

The desosamine/mycaminose moiety at the C5 position makes specific hydrogen bond interactions with the nucleotide residues A2058 and A2059 (E. coli numbering). Furthermore, for those macrolides that possess a sugar at the C3 position, this cladinose group makes specific interactions with the base of nucleotide 2505, though this only contributes incrementally to the affinity of the macrolide for the 50S subunit (Hansen et al., 2002).

Various additional substitutions on the macrolactone ring are observed. Figure 1 shows the chemical structures of two macrolides - pikromycin and erythromycin with their glycosylations.

Figure 1. 2D structures of some of the naturally derived macrolide antibiotics (pikromycin and erythromycin). Structures were drawn using ChemAxon.
Figure 1. 2D structures of some of the naturally derived macrolide antibiotics (pikromycin and erythromycin). Structures were drawn using ChemAxon.

Types

Macrolide antibiotics are classified according to the size of the macrocyclic lactone ring - i.e., are they 12‐, 14‐, 15‐, or 16‐membered rings (Dinos, 2017). Since its discovery in the 1950s, many derivatives of the 14-membered macrocycles (erythromycin and pikromycin) have been synthesized (Figure 1). This second generation of macrolides includes 14-membered clarithromycin and 15-membered azithromycin (Figure 2). The third generation of macrolides, known as ketolides (e.g., Telithromycin, Figure 2), was developed as a result of rising cases of macrolide resistance. Here the cladinose sugar linked to the C3 position is replaced by a 3-keto group (Amdan et al., 2024).

Figure 2. Examples of second and third generation of macrolides - Azithromycin and Telithromycin. The figure was drawn using ChemAxon.
Figure 2. Examples of second and third generation of macrolides - Azithromycin and Telithromycin. The figure was drawn using ChemAxon.

Despite the chemical diversity of macrolides, there is an extensive similarity in how they bind to the ribosome (Figure 3, Bulkley et al, 2010). Note that the the structures of Thermus thermophilus ribosome in complex with different types of macrolides show binding near U2611, A2058, and A2059 of the 23S RNA, near the ribosomal exit tunnel. While the lactone rings of erythromycin (Figure 3A), azithromycin (Figure 3B), and telithromycin (Figure 3C) bind in relatively the same position and orientation the alkyl-aryl moiety in telithromycin extends beyond the binding site of the former two.

Figure 3. Structures of Thermus thermophilus ribosome complexed with different macrolides (Bulkley et al, 2010). A. Bound to erythromycin (PDB ID 4v7x); B. Bound to azithromycin (PDB ID 4v7y); C. Bound to Telithromycin (PDB ID 4z7z)
Figure 3. Structures of Thermus thermophilus ribosome complexed with different macrolides (Bulkley et al, 2010). A. Bound to erythromycin (PDB ID 4v7x); B. Bound to azithromycin (PDB ID 4v7y); C. Bound to Telithromycin (PDB ID 4z7z)

Resistance

The first report of erythromycin resistance was discovered in Staphylococcus aureus in the Minneapolis General Hospital in 1953, just a few months after erythromycin was introduced for clinical use (Wise et al., 1955). Since then, macrolide resistance has been detected in various types of bacteria. Various mechanisms by which bacteria can develop resistance against macrolide antibiotics have been studied (Amdan et al., 2024), including:
* target modification, specifically at the 23S rRNA binding site
* antibiotic efflux (e.g., for azithromycin)
* target (ribosome) protection
* antibiotic modifications

Key players in the last two resistance mechanisms are briefly described here.

Target Protection

A group of proteins called the antibiotic resistance (ARE) ATP-binding cassette F (ABC-F) proteins confer resistance to several antibiotics that target the peptidyl-transferase center (PTC) and nascent peptide exit tunnel (NPET) in the ribosome. An example of a protein that has been implicated in macrolide resistance is called MsrE. The msr genes have been identified in staphylococci, streptococci, and enterococci, and have recently spread to P. aeruginosa. The MsrE proteins have been shown to bind to the ribosomal exit site, preventing antibiotic binding, and increasing azithromycin resistance (Figure 4, Su et al., 2018). Note that the binding of MsrE is close to where macrolides would bind (see Figure 4, right)

Figure 4. The structure of ABC-F protein MsrE (PDB ID 5zlu, Su et al., 2018) shows the binding of the MsrE protein (green) alongside the P-site tRNA (red). The 16S rRNA is colored in pink while the 23S and 5S rRNA are colored in blue. All ribosomal proteins are colored grey.
Figure 4. The structure of ABC-F protein MsrE (PDB ID 5zlu, Su et al., 2018) shows the binding of the MsrE protein (green) alongside the P-site tRNA (red). The 16S rRNA is colored in pink while the 23S and 5S rRNA are colored in blue. All ribosomal proteins are colored grey.

Antibiotic modifications

Three types of macrolide modification enzymes have been identified that lead to resistance:

* Macrolide glycosyltransferases
This enzyme adds a glycosyl group to the macrolide antibiotic altering its chemical properties, structure, and function. The glycosylation is carried out in the presence of UDP-glucose, as the glucose donor. The structure shown in Figure 5A has UDP bound to the enzyme (PDB ID 2iyf, Bolam et al., 2007).

* Macrolide phosphotransferases
This enzyme adds a phosphate group to the macrolide antibiotic altering its chemical properties, structure, and function. The phosphorylation uses GTP as the source of the phosphate group. The structure shown in Figure 5B has GDP bound to the enzyme (PDB ID 5igp, Fong et al. 2017)

* Macrolide esterases
This enzyme breaks the macrolactone ring destroying the structure of the antibiotic. The proposed site for erythromycin binding is marked with a light pink circle. (Figure 5C, PDB ID 6xcq, Zieliński et al., 2021).

Figure 5: three different macrolide inactivation enzymes that lead to resistance. A. A macrolide glycosyltransferases in complex with erythromycin and UDP (PDB ID 2iyf, Bolam et al., 2007); B. Macrolide phosphotransferase in complex with erythromycin and GDP (PDB ID 5igp, Fong et al., 2017); C. Erythromycin esterase (PDB ID 6xcq, Zieliński et al., 2021) All structures are represented as cartoons, colored using the rainbow color scheme denoting N- to C- direction of the polymer chain (from blue to red). Ligands are shown in ball and stick representation.
Figure 5: three different macrolide inactivation enzymes that lead to resistance. A. A macrolide glycosyltransferases in complex with erythromycin and UDP (PDB ID 2iyf, Bolam et al., 2007); B. Macrolide phosphotransferase in complex with erythromycin and GDP (PDB ID 5igp, Fong et al., 2017); C. Erythromycin esterase (PDB ID 6xcq, Zieliński et al., 2021) All structures are represented as cartoons, colored using the rainbow color scheme denoting N- to C- direction of the polymer chain (from blue to red). Ligands are shown in ball and stick representation.

Another enzyme that was recently found to modify macrolides is a serine dependent α/β-hydrolase (Dhindwal et al. 2023). No structures of this enzyme is available at the time of this writing.

Learn more about the other resistance mechanisms in the context of azithromycin resistance.

References

Amdan, N. A. N., Shahrulzamri, N.A., Hashim, R., Mohamad, J. N. (2024) Understanding the evolution of macrolides resistance: A mini review. J Glob Antimicrob Resist. 38:368-375. https://doi.org/10.1016/j.jgar.2024.07.016

Bolam, D. N., Roberts, S., Proctor, M. R., Turkenburg, J. P., Dodson, E. J., Martinez-Fleites, C., Yang, M., Davis, B. G., Davies, G. J., Gilbert, H. J. (2007) The crystal structure of two macrolide glycosyltransferases provides a blueprint for host cell antibiotic immunity. Proc Natl Acad Sci U S A. 104(13):5336-41. https://doi.org/10.1073/pnas.0607897104

Bulkley, D., Innis, C. A., Blaha, G., Steitz, T. A. (2010) Revisiting the structures of several antibiotics bound to the bacterial ribosome. Proc Natl Acad Sci U S A. 107(40):17158-63. https://doi.org/10.1073/pnas.1008685107

Dhindwal, P., Thompson, C., Kos, D., Planedin, K., Jain, R., Jelinski, M., Ruzzini, A. (2023) A neglected and emerging antimicrobial resistance gene encodes for a serine-dependent macrolide esterase. Proc Natl Acad Sci U S A. 120(8):e2219827120. https://doi.org/10.1073/pnas.2219827120

Dinos, G. P. (2017) The macrolide antibiotic renaissance. Br J Pharmacol. 174(18):2967-2983. https://doi.org/10.1111/bph.13936

Fernandes, P., Martens, E. Pereira, D. (2017) Nature nurtures the design of new semi-synthetic macrolide antibiotics. J Antibiot 70, 527–533 https://doi.org/10.1038/ja.2016.137

Fong, D. H., Burk, D. L., Blanchet, J., Yan, A. Y., Berghuis, A. M. (2017) Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance. Structure. 25(5):750-761.e5. https://doi.org/10.1016/j.str.2017.03.007

Golkar, T., Zieliński, M., Berghuis, A. M. (2018) Look and Outlook on Enzyme-Mediated Macrolide Resistance. Front Microbiol. 9:1942. https://doi.org/10.3389/fmicb.2018.01942

Su, W., Kumar, V., Ding, Y., Ero, R., Serra, A., Lee, B. S. T., Wong, A. S. W., Shi, J., Sze, S. K., Yang, L., Gao, Y. G. (2018) Ribosome protection by antibiotic resistance ATP-binding cassette protein. Proc Natl Acad Sci U S A. 115(20):5157-5162. https://doi.org/10.1073/pnas.1803313115

Wise, R. I., Voigt, A. E., Collin, M. V., Cranny, C. L. (1955) Origin of Erythromycin-Resistant Strains of Micrococcus Pyogenes in Infections: Bacteriophage Types and In Vitro Resistance of Cultures to Antibiotics. AMA Arch Intern Med. 95(3):419–426. https://doi.org/10.1001/archinte.1955.00250090057008

Zieliński, M., Park, J., Sleno, B., Berghuis, A. M. (2021) Structural and functional insights into esterase-mediated macrolide resistance. Nat Commun. 12(1):1732. https://doi.org/10.1038/s41467-021-22016-3

March 2025, Shuchismita Dutta; Reviewed by Drs. Albert Berghuis and Tolou Golkar
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/prot-syn/ribo/MCL