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Understanding biological membranes: From cell biology to antimicrobial materials

Primary Supervisor: Professor Sebastien Perrier, Department of Chemistry

Secondary supervisor: Professor Meera Unnikrishnan

PhD project title: Understanding biological membranes: From cell biology to antimicrobial materials

University of Registration: University of Warwick

Project outline:

Multi-drug resistant bacteria are one of the major causes of death globally, jeopardising the effectiveness of modern medicine. Infections caused by ESKAPE pathogens (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are especially concerning for their high mortality risk. In the last 20 years only six new classes of antibiotics have reached the clinic and none of them are active against Gram-negative bacteria.

Bacterial pathogens are able to quickly evolve resistance against conventional small molecule antibiotics with single cellular targets or modes of action. This often arises from the modification of the target molecules in the cell. Inspired by nature, researchers have focussed on antimicrobial peptides (AMPs) as an alternative attempt to tackle the global antimicrobial crisis. AMPs are short amphipathic amino acid chains with cationic and hydrophobic moieties, which possess broad antimicrobial activity against Gram-positive and Gram-negative bacteria, fungi, viruses, and parasites. One of the predominant mechanisms of action of AMPs is the disruption of bacterial membrane integrity. This is mediated by electrostatic interactions between negatively charged moieties on the bacterial surface with positively charged residues within AMPs, combined with the hydrophobic AMP side chains driving insertion into the bacterial membrane. Additionally, AMPs have been observed to translocate through the membrane to the cytoplasm, where binding to intracellular targets such as DNA, RNA and proteins leads to bacterial cell death. The presence of multiple targets, together with the large fitness cost incurred by changes in components of the cell surface, makes the emergence of resistance against AMPs rare.

Even though AMPs are promising candidates as antimicrobial agents, cytotoxic effects against mammalian cells have been reported, due to their inherent ability to disrupt lipid bilayers, and therefore cell membranes. Their application is hindered further by their proteolytic instability and the high cost associated to their synthesis. The limitations of AMPs have resulted in an increasing interest in the development of synthetic antimicrobial peptides (sAMPs). Common strategies of sAMPs development include single amino acid substitutions, segmentation of AMPs to obtain smaller active fragments and chimera generation, the incorporation of unnatural amino acids and in silico methods to predict new synthetic peptides. More recently, polymeric materials have also been exploited as AMP mimics in order to overcome some of the above limitations. Precision polymer chemistry enables the development of sAMPs, with functionalities precisely positioned in the structure to enhance antimicrobial activity whilst mitigating toxicity towards mammalian cells.

Our team has developed synthetic techniques to build libraries of sAMPs that act as synthetic mimics of antimicrobial peptides. We study both the disruptive effect these systems have on bacterial membranes and their interactions with mammalian cell membranes. By employing our systems as probes, we can elucidate fundamental mechanisms involved in both bacterial and mammalian cells membranes. We also use machine learning to inform the design of sAMPs, based on materials design and resulting properties and activities. We then exploit our findings to tune the sAMPs towards high antimicrobial activity and low cell toxicity. Membrane interactions are studied with a range of characterisation techniques, including electron microscopy, membrane polarisation experiments, neutron and X-Ray scattering . sAMPs are then tested for their antimicrobial properties, using media that mimic clinically relevant conditions, against Gram-positive and Gram-negative bacteria. We have shown that media composition can have an important influence on activity. We have developed algorithms for machine learning to identify optimal the structure-property relationships and target lead candidates, which are then tested in vivo, and activity and pharmacokinetic parameters are established. Applications of our systems range from mycobacteria (e.g. TB) to biofilm formation inhibition.

This truly multidisciplinary PhD project will cover these topics and offer training in all these disciplines, with focus depending on the research interests of the candidate.

BBSRC Strategic Research Priority: Understanding the Rules of Life: Microbiology

    Techniques that will be undertaken during the project:

    • Techniques include:
    • Synthetic chemistry
    • Material characterisation
    • Lipid bilayer characterisation via microscopy, neutron nd x-ray scattering, membrane depolarisation, etc
    • Typical cell culture and cell toxicity assays (eg XTT)
    • Typical microbiology techniques such as bacterial culture, MIC determination etc
    • Computing and programming for machine learning

    Contact: Professor Sebastien Perrier, University of Warwick