Supramolecular Protective Groups Enabling Antibiotics and Bioimaging

Project Information

SUPRABIOTICS

Grant agreement ID: 694610

DOI

10.3030/694610

Project closed

EC signature date 20 April 2016

Start date 1 September 2016

End date 31 January 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

DWI LEIBNIZ-INSTITUT FUR INTERAKTIVE MATERIALIEN EV
Germany

Periodic Reporting for period 4 - SUPRABIOTICS (Supramolecular Protective Groups Enabling Antibiotics and Bioimaging)

Reporting period: 2020-10-01 to 2022-01-31

Summary of the context and overall objectives of the project

The pharmaceutical sector has a huge demand for new active compounds including natural products to fill the drug pipelines and to stop the global decline in novel approved active pharmaceutical ingredients. Therefore, developing new tools to fabricate complex molecular structures in a fast and reliable way is paramount. This holds especially true for the field of antibiotics. Multidrug resistant (MDR) pathogens evolve at a terrifying rate and confer resistance to all presently available antibacterial treatments, leading the WHO to condemn MDR bacteria as a major threat to human health.
In this ERC Advanced Grant, new approaches to fabricate very complex molecules with minimal synthetic effort were pursued. The technology is based on nucleic acid binders (aptamers), which are evolved to bind a target molecule and block several functional groups within that molecule while allowing other functionalities not in contact with the aptamer to be selectively modified in a single reaction step. Here, we aim to establish this technology as a novel tool that gives access to compounds that are difficult to obtain by conventional synthesis. The resulting compounds were employed as novel antibiotics that kill MDR bacteria and as imaging reagents for infections as well as RNA molecules in live cells.

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 course of the project, we have further expanded the aptamer protective group (APG) technology that allows fabrication of complex natural products with minimal synthetic effort. In this regard, we have demonstrated that the APG technology is compatible with multiple different reactions and reagents. Moreover, we have synthesized labelled aminoglycoside antibiotics, which selectively stain gram-negative bacteria and therewith allow bioimaging of gram-negative infections in vivo. Additionally, we have fabricated antibiotics that can be switched by light between two states. In one state, they allow to kill resistant bacteria while in the other state they are not active against these pathogens. Similarly, photo-switchable bioactives have been employed to photo-chemically control gene expression together with RNA-based riboswitches. As another trigger to switch on drugs and in particular different classes of antibiotics, ultrasound was employed. Ultrasound acts as a molecular scalpel to selectively cleave covalent and supramolecular bonds to activate proteins and antibiotics with high spatiotemporal control. Finally, we have fabricated probes that rely on antibiotic compounds, which allow the improved visualization of RNA in living mammalian cells.
The results of this research have been communicated in more than 40 papers and presented on many scientific conferences.

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)

So far aptameric protective groups were only employed to produce derivatives of aminoglycosides containing amide and urethane bonds. In this action, we have significantly broadened the scope of reactions and reagents for this late stage modification technology. So far, no photo-switchable aminoglycoside antibiotics were known. In this grant, we fabricated for the first time aminoglycosides that can be switched by light and by this means kill resistant bacteria or function as light-sensitive bioactives to photo-control translation of proteins. Moreover, we demonstrated for the first time that drugs including aminoglycoside antibiotics can be activated by ultrasound as an external trigger. This might allow sptiotemporal control over drug action in the future with the fascinating perspective of reducing the development of antibiotic resistant bacteria and side effects in patients.
Bacteria are classified in gram-positive and gram-negative ones, which is important for antibiotic treatment. We present an unprecedented staining reagent that allows staining of gram-negative bacteria and at the same time functions as a bioimaging reagent in vivo without contributing to resistance development.
Finally, we have developed probes that allow the visualization of RNA in living cells. Before, these probes were less selective due to low binding affinities, moderately entered cells and exhibited low solubility in water. Our new probes overcome these shortcomings.

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