Catalytic Antibiotic Activation: Tackling Resistance with Artificial Metalloenzymes

Background:

Antimicrobial resistance is a global health crisis and new antibacterial strategies are urgently needed, including methods for the targeted activation of antibiotics in pathogenic bacteria. Since bacterial cells rely on species-specific siderophores (Greek: iron carriers) for the uptake of essential iron(III), whilst human cells do not, bacteria can be targeted based on the type of siderophore they utilise. Hence, siderophore-based targeting allows for the killing of specific pathogenic bacteria, thereby avoiding indiscriminate exposure that damages the microbiome and spreads resistance. Another layer of specificity can be provided by the targeted siderophore-mediated insertion of artificial metalloenzymes (as ‘Trojan horses’) into pathogenic cells, thereby enabling bioorthogonal reactions that have no equivalent in biology to be used for the catalytic activation of antibiotic prodrugs [1]. In this way, only bacterial target cells are killed.

Objectives:

The project aims at using pathogen-specific siderophores to smuggle synthetic ruthenium-based catalysts into pathogenic bacteria where they act as bioorthogonal artificial enzymes for the activation of antibacterial prodrugs. Individual objectives include the design and synthesis of siderophore-linked deallylation catalysts, the development of allyl-protected prodrugs that can be uncaged by these ruthenium-based catalysts to release the active antibiotics, and the assessment of the resulting antimicrobial activity.

Experimental approach:

A series of ruthenium-binding ligands will be chemically synthesised, derivatised with a linker for siderophore attachment and bound to suitable catalyst precursors using inert gas techniques. The resulting deallylation catalysts will be optimised through ligand modifications to maximise catalytic activity. The choice of siderophore is guided by siderophore transporters expressed by the target pathogen and the availability of functional groups that allow for chemical conjugation, e.g. via amide bonds or click chemistry. In addition, a selection of antibacterial prodrugs will be synthesised by converting amine or carboxylic acid groups in the pharmacophores of active antibiotics to allyl carbamates or allyl esters, thereby inactivating them. Examples include fluoriquinolones and beta-lactam antibiotics. 

A panel of key bacterial strains will be used to investigate if exposure to the siderophore-linked catalysts makes bacterial cells sensitive to killing by the prodrugs. Cells not exposed to the catalysts serve as controls. To gauge potential side effects, the cytotoxicity of the prodrugs and the siderophore-linked catalysts will be tested against human cells. 

Novelty:

Recent advances in bioorthogonal chemistry have led to the development of synthetic catalysts that enable nonbiological chemical reactions to be performed selectively inside living cells [2]. Our approach of targeting these ‘artificial enzymes’ to pathogenic bacterial cells is novel and gives access to new prodrug activation reactions that provide an unprecendeted level of selectivity. 

Training:

This project provides multidisciplinary training in research skills at the interface between medicinal chemistry and clinical microbiology, drawing upon bio-orthogonal chemistry, catalysis and antimicrobial resistance research. The successful candidate will learn to design and synthesise antimicrobial compounds, to execute suitable experiments to aid antimicrobial drug discovery, study kinetic and resistance mechanisms, critically evaluate the results and develop team-working, time-management and presentation skills. This hands-on training will be complemented by suitable graduate training courses. The student will participate regular group and section meetings, and is encouraged to attend at least two relevant conferences.

Applicants should have a background in synthetic chemistry and catalysis and be willing to learn the microbiological aspects of the project.

References:

[1] J. W. Southwell, A.-K. Duhme-Klair et al., Siderophore-Linked Ruthenium Catalysts for Targeted Allyl Ester Prodrug Activation within Bacterial Cells, Chem. Eur. J. (2022), doi.org/10.1002/chem.202202536.

[2] A. Seoane, J. L. Mascarenas, Exporting Homogeneous Transition Metal Catalysts to Biological Habitats, Eur. J. Org. Chem. (2022), doi.org/10.1002/ejoc.202200118.

All Chemistry research students have access to our innovative Doctoral Training in Chemistry (iDTC): cohort-based training to support the development of scientific, transferable and employability skills: https://www.york.ac.uk/chemistry/postgraduate/training/idtc/ 

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For more information about the project, click on the supervisor's name above to email the supervisor. For more information about the application process or funding, please click on email institution

This PhD will formally start on 1 October 2023. Induction activities may start a few days earlier.

To apply for this project, submit an online PhD in Chemistry application: https://www.york.ac.uk/study/postgraduate/courses/apply?course=DRPCHESCHE3