Prof. dr. Eefjan Breukink

• 

  prof. dr. E.J. (Eefjan) Breukink

  Email: e.j.breukink@uu.nl

  Phone: 030 253 3523

  Address

  Padualaan 8
  3584CH Utrecht

The fight against resistant microbes

The invention of antibiotics is considered one of the greatest triumphs of medicine, saving millions of lives every year. However, bacteria and fungi are getting more and more resistant towards these antibiotics, and this resistance is an ever increasing worldwide problem, which needs more efforts in developing novel ways to treat infections caused by these resistant bacteria. Indeed, the World Health Organization has called for the development of novel antibacterial therapies that are less susceptibility to antibiotic resistance (WHO, 2023). Especially the development of novel antibiotics targeting Gram-negative bacteria would lead to a reduction in AMR burden, and the WHO has highlighted Enterobacteriaceae (including K. pneumoniae and E. coli) and Acinetobacter baumannii that have become carbapenem-resistant as the most critical AMR global health threats. We try to contribute to this fight against the resistant microbes by using the following approaches.

1. Learn from existing antibiotic compounds and try to make them better
2. Devise novel screening approaches
3. Selectively fish for novel compounds that target the best antibiotic target ever….

Bacterial cell wall synthesis

The bacterial cell wall synthesis pathway is the most accessible essential pathway of bacteria and hence a very important target for antibiotic development (see figure below). 

Central to the pathway is a polyisoprenoid based precursor, called Lipid II that shuttles the basic building block of the cell wall or better the peptidoglycan layer across the plasma membrane of bacteria. Lipid II is then used by bi-functional penicillin binding proteins (PBPs) for the synthesis of the peptidoglycan network. This essential role of Lipid II, its uniqueness to bacteria and the fact that it is NOT a protein (thus less prone to be changed by singe mutations on the DNA) makes it an ideal antibiotic target.

Mode of action of (Lipid II targeting) antibiotics

We are especially interested in determining the modes of action of molecules that target the bacterial cell wall biosynthesis machinery and Lipid II in particular. We focus (in collaboration with the Weingarth group) on the structural elucidation of the antibiotic-Lipid II complexes. Examples you can find in the following references:

• https://doi.org/10.1038/s41564-024-01696-9
• https://doi.org/10.1016/j.cell.2023.07.038
• https://doi.org/10.1038/s41586-022-05019-y
• https://doi.org/10.1038/s41467-018-06314-x

From this information we try to improve the activity of these molecules e.g. by chemically modifying them.

Finding novel antibiotics targeting Gram-negative bacteria

Gram-negative bacteria are especially difficult to target due to the major distinguishable feature with their Gram-positive counterparts: the (extra) outer membrane (OM) within their cell envelope structure. The Gram-negative outer membrane acts as a formidable permeability barrier for antibiotic compounds and is the main reason why infections caused by Gram-negative bacteria are much more difficult to treat than those caused by Gram-positive bacteria. The outer membrane directly interacts with the external environment, and is essential for bacterial viability, thus the outer membrane itself and its biogenesis are interesting targets for antibiotic development.

In order to identify novel antibiotics we are developing HT-capable whole-cell based screening assays that are designed to identify antibacterial compounds that act specifically on the outer membrane and/or the biogenesis pathways of its essential and characteristic constituents, i.e. the lipoproteins, the outer membrane proteins (OMPs) and lipopolysaccharides (LPS).

Lipid II targeting antibiotics

The essential cell wall precursor lipid II is a very interesting target for antibiotic development. In collaboration with the Fungal Biodiversity Centre (CBS) of the KNAW, we are screening fungal extracts for novel antibiotics that act on Lipid II. We aim to fully elucidate the structural characteristics of the molecules that are active at the level of Lipid II, identify the responsible biosynthetic gene clusters, and produce them in a “clean” host strain. Furthermore, we aim to determine their toxicity towards mammalian cells and (provided that they are not toxic) their activity in infection models. Ultimately, we aim to bring at least one novel antibiotic to the clinic.