Markus Weingarth, a biochemist at Utrecht University, considers lipid II, a building block of bacteria cell walls, one of the most promising antibiotic targets. Human cells don’t produce it — so targeting it avoids toxicity — and bacteria struggle to develop resistance against it. 

His research group recently published a study in Nature Microbiology, in which they reported that the antibiotic plectasin binds lipid II by forming dense structures on bacterial membranes (1). The findings improve researchers’ understanding of how lipid II binding disrupts the cell walls of bacteria, which can help them develop better antibiotics.

Novozyme’s scientists first described plectasin’s mechanism of action in 2010 (2). However, in their experiments, they used artificial membranes called micelles and showed that each plectasin molecule paired with one lipid II molecule. However, micelles do not accurately mimic the membrane environment. “We took a gamble, believing that what happened in micelles was not the real deal, and this turned out to be the case,” said Weingarth. In biological membranes, the team found that plectasin formed massive supramolecular structures upon lipid II binding. “We saw that the supramolecular mechanism was not the exception, but rather the rule among the lipid II binders.”

How is plectasin’s mechanism of action different from that of other antibiotics?

Conventional antimicrobial peptides selectively bind bacteria based on electrostatics, as bacterial membranes are negatively charged while human cell membranes are positively charged. This electrostatic interaction is fairly unspecific. However, plectasin targets lipid II specifically based on both structure and charge, making it a highly selective target binder. This specificity marks its first major difference. Most drugs follow a conventional "one drug, one target" mechanism, where the drug and the target interact directly. In contrast, plectasin and other lipid II binders form massive supramolecular structures upon target binding. This formation is not just a feature but a critical aspect of the mechanism. Without these superstructures, there would be no stable target binding. These two prominent features of plectasin — highly specific interaction with the target and supramolecular recognition — distinguish it from conventional antimicrobial peptides.

The other thing that stands out about plectasin’s mechanism is that it is calcium modulated, which was an unexpected discovery. In hindsight, it seems obvious given the presence of a large ionic pocket that naturally binds calcium. However, this aspect had not been mentioned in any previous publications on plectasin.

What makes lipid II a good antibiotic target?

Lipid II has fatty acid tails and a pyrophosphate head group, which bacteria cannot alter. There are no known cases of bacteria replacing the pyrophosphate group for peptidoglycan synthesis, making it an absolute bottleneck for their cell wall biosynthesis. However, bacteria might be able to develop indirect resistance mechanisms, such as making the target inaccessible. They could make the peptidoglycan layer so dense that the drug never reaches the target. This is energy-intensive and unstable. Additionally, bacteria cannot make more lipid II once it’s captured, so targeting lipid II at these immutable sites makes it difficult for bacteria to develop stable resistance mechanisms.

We saw that the supramolecular mechanism was not the exception, but rather the rule among the lipid II binders. 
– Markus Weingarth, Utrecht University

How effective is plectasin as an antibiotic?

Plectasin is not effective against gram-negative bacteria because it cannot overcome their outer membrane. However, plectasin is highly efficient against gram-positive bacteria and maintains this effectiveness in animal models of infection. Despite its potential as a relevant therapeutic, I am pessimistic about its future because the clinical development of plectasin was discontinued, and the work was never published. However, plectasin ticks many important boxes: It is stable in serum, non-cytotoxic, and highly efficient against a broad range of superbugs, including in animal models of infection, making it a compelling clinical candidate.  

Although plectasin’s future as a therapeutic is uncertain, the study’s findings have significant implications for the design of lipid II-binding antibiotics. It’s crucial to optimize both the part of the drug that binds the target and the part responsible for oligomerization. This aspect has been ignored so far, as the focus has traditionally been on target binding alone. However, target binding and oligomerization are strongly interdependent. Only when both are optimized can ideal target binding occur.

This interview has been condensed and edited for clarity.

References

1. Jekhmane, S. et al. Host defence peptide plectasin targets bacterial cell wall precursor lipid II by a calcium-sensitive supramolecular mechanism. Nat Microbiol  9, 1778–1791 (2024).
2. Schneider, T. et al. Plectasin, a Fungal Defensin, Targets the Bacterial Cell Wall Precursor Lipid II. Science  328, 1168–1172 (2010).