Determining the mechanisms of lipid-targeting antibiotics in intact bacteria

Project Information

champANTIBIOTICS

Grant agreement ID: 101045485

DOI

10.3030/101045485

EC signature date 25 May 2022

Start date 1 June 2022

End date 31 May 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 000 000,00

EU contribution

€ 2 000 000,00

Coordinated by

UNIVERSITEIT UTRECHT
Netherlands

Periodic Reporting for period 1 - champANTIBIOTICS (Determining the mechanisms of lipid-targeting antibiotics in intact bacteria)

Reporting period: 2022-06-01 to 2024-11-30

Summary of the context and overall objectives of the project

Antimicrobial resistance poses a grave threat to human health. Various pathogens, including M. tuberculosis and methicillin-resistant S. aureus (MRSA), have become resistant to most antibiotics. Without new intervention strategies, this could cause up to 10 million deaths/yr. This issue is exacerbated by a drought in the antibiotic pipeline, with alarmingly few new classes of antibiotics introduced over the past decades. To ensure the future availability of therapeutics, there is an acute need for new antibiotics that use unexploited mechanisms. However, antibiotic development is hampered by a fundamental lack of mechanistic insight into some of the most promising drugs. This project aims to address this knowledge gap.

Ideal candidates for next-generation drugs could be lipid-targeting that target special lipids that only exist in bacterial, but not in human cell membranes. LT-antibiotics kill a broad spectrum of superbugs and are robust to resistance because their conserved lipid targets are difficult to modify.

In this project, we aim to develop new tools to determine the mechanism of antibiotics that target bacterial membranes. Here, we follow three major objectives

• Objective 1: Determine the mechanisms of novel drugs recently discovered in so-called ‘unculturable’ bacteria.

• Objective 2: Elucidate the molecular mechanism of daptomycin, a last-resort antibiotic of major clinical importance whose elusive binding mode has been controversial for decades.

• Objective 3: Develop tools to study the native binding modes of antibiotics in bacterial membranes and intact bacteria.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first two years of our ERC project, we succeeded to make important advances towards a better understanding of Lipid-targeting antibiotics.
The most notable achievements are three publications that deal with the modes of action of antibiotics that target bacterial cell precursors (such as Lipid II) that are embedded in the bacterial plasmamembrane. We could show on the examples of Teixobactin (Shukla et al., Nature 2022, doi: 10.1038/s41586-022-05019-y) Clovibactin (Shukla et al., Cell 2023, doi: 10.1016/j.cell.2023.07.038) and Plectasin (Jekhmane, Derks et al., Nature Microbiology 2024, doi: 10.1016/j.cell.2023.07.038) that these antibiotics target cell wall precursors by assembling into massive supramolecular structures on the membrane-surface. The formation of suprastructures upon target binding is a striking departure from the conventional 1: 1 target paradigm. Thereby, our research opens new avenues for the design of better antibiotics.

On the technological side, our insights were enabled by conceiving a new integrative structural biology approach that combines state-of-the-art solid-state NMR spectroscopy with advanced (confocal and high-speed atomic force) microscopy approaches. Together, these methods enabled to study the action of cell-wall precursor targeting antibiotics across several length-scales (sub-micrometre to angstrom). This was essential to investigate the supramolecular mechanisms of lipid-targeting antibiotics.
Furthermore, we have made important inroads towards a better understanding of daptomycin, and we are confident to make further progress in this direction.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The most important result of our research is that we could demonstrate that antibiotics that target cell wall precursors do so using supramolecular mechanisms on the bacterial membrane surface. This is a striking departure from the conventional one ligand–one target paradigm, which was believed to be the common mechanism for these antibiotics. Thereby, our research opens new avenues for the design of better antibiotics.

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