Transpeptidase substrate

The cell wall of gram-positive bacteria is primarily formed of peptidoglycans and is susceptible to the effects of glycopeptide antibiotics (Reynolds, 1989). Gram-negative bacteria have an outer lipid membrane, which vancomycin-like antibiotics cannot penetrate, making them insensitive to this class of antibiotics.

The last step of peptidoglycan biosynthesis is the transpeptidation. Instead of targeting the enzyme (like the β-lactam antibiotics), glycopeptide antibiotics bind to the substrate of this enzyme. This transpeptidase substrate is thus the target of several antibiotics in this class that are in clinical use - e.g., vancomycin, teicoplanin, oritavancin, telavancin, and dalbavancin.

Function

The target of glycopeptide antibiotics is the D-Ala-D-Ala group at the C-terminus of the uridine diphosphate N-acetylmuramic acid pentapeptide. This pentapeptide is a building block of the cell wall peptidoglycan. Once it is incorporated into a growing peptidoglycan chain, the D-Ala-D-Ala group forms cross-links with adjacent peptidoglycan strands in the cell wall, significantly strengthening the resulting matrix of peptidoglycan (Figure 1). Enzymes that carry out this process are known as transpeptidases. These enzymes catalyze the formation of a covalent bond between the penultimate D-Ala residue on one strand and a peptide on the adjacent strand (Lovering, Safadi, and Strynadka, 2012).

Learn more about cell wall and peptidoglycan biosynthesis.

Figure 1. Cartoon depicting the cross-linked structure of the peptidoglycan layer, represented by the line connecting the blue and green spheres.
Figure 1. Cartoon depicting the cross-linked structure of the peptidoglycan layer, represented by the line connecting the blue and green spheres.

Structure

The transpeptidase substrate is a pentapeptide, where the C-terminal 3 amino acids are targeted by the glycopeptide antibiotic (Figure 2, Nitanai et al., 2009). Note that the D-Ala-D-Ala part of the peptide forms 5 hydrogen bonds with the vancomycin. Additional water-mediated hydrogen bonds also stabilize this structure (not shown here for clarity). Any change in the structure of the transpeptidase substrate can alter its binding to vancomycin, making it resistant. Learn more about vancomycin.

Figure 2. Structure of vancomycin with di-acetyl-L-Lys-D-Ala-D-Ala, an analog of the transpeptidase substrate (PDB ID 1fvm, Nitanai et al., 2009). The 5 hydrogen bonds are numbered 1-5. the vancomycin is shown with a semi-transparent surface, while the substrate is shown in ball and stick representation (with carbon atoms colored in shades of pink).
Figure 2. Structure of vancomycin with di-acetyl-L-Lys-D-Ala-D-Ala, an analog of the transpeptidase substrate (PDB ID 1fvm, Nitanai et al., 2009). The 5 hydrogen bonds are numbered 1-5. the vancomycin is shown with a semi-transparent surface, while the substrate is shown in ball and stick representation (with carbon atoms colored in shades of pink).

Pharmacological Implications

When vancomycin, the first glycopeptide antibiotic, was discovered, it faced concerns about toxicity, which were traced to impurities in the early formulations. Improved purification methods overcame many of these issues, although the drug continues to have a narrow therapeutic window, necessitating careful monitoring. Improved purification methods overcame many of these issues, although the drug continues to have a narrow therapeutic window, necessitating careful monitoring. Vancomycin was found to be very effective in treating gram-positive bacterial infections, and it became widely used as a last-resort antibiotic, employed when other antibiotics failed. Its usage expanded greatly in response to the rise of methicillin-resistant Staphylococcus aureus in the 1980s. This in turn triggered an increase in vancomycin resistance, which raises questions about the continuing efficacy of this molecule. However, the creation of novel semi-synthetic derivatives has revived interest in this class of antibiotics as effective therapeutic agents (Blaskovich et al., 2018).

References

Blaskovich, M. A. T., Hansford, K. A., Butler, M. S., Jia, Z., Mark, A. E., Cooper, M. A. (2018) Developments in Glycopeptide Antibiotics. ACS Infect Dis. 4(5):715-735. https://doi.org/10.1021/acsinfecdis.7b00258

Lovering, A. L., Safadi, S. S., Strynadka, N. C. (2012). Structural perspective of peptidoglycan biosynthesis and assembly. Annual review of biochemistry, 81, 451–478. https://doi.org/10.1146/annurev-biochem-061809-112742

Nitanai, Y., Kikuchi, T., Kakoi, K., Hanamaki, S., Fujisawa, I., Aoki, K. (2009) Crystal structures of the complexes between vancomycin and cell-wall precursor analogs. J Mol Biol. 385(5):1422-32. https://doi.org/10.1016/j.jmb.2008.10.026

Reynolds P. E. (1989). Structure, biochemistry and mechanism of action of glycopeptide antibiotics. European journal of clinical microbiology & infectious diseases, 8, 943–950. https://doi.org/10.1007/BF01967563

March 2025, Sameer Ahmad, Shuchismita Dutta; Reviewed by Dr. Patrick Loll
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/cellwall-biosynth/trpep