Gram-scale production of antibacterial cyclic peptide via a synthetic biology approach

Antibacterial cyclic peptides are known for their high stabilities and can be used as anti-microbials for treating gastrointestinal infections, including ones caused by multi-drug resistant pathogens.

This project will use an interdisciplinary approach to make cyclic peptides libraries at large scales and screen for their antibacterial properties.

We are seeking for a self-motivated and intelligent PhD student to help address a key global challenge – designing and producing novel antibacterial agents – by using a mixture of microbiology, biocatalysis, computational chemistry and chemical biology techniques.

The use of active cyclic peptides as pharmaceuticals has become the frontier for drug discovery. Natural cyclic peptides confer a wide range of biological activity, whereas de novo designed cyclic peptides incorporated with unnatural amino acids are shown to be potent modulators for "undruggable" targets. Noticeably, because of their stabilities against acid and protease treatments, antibacterial cyclic peptides are particularly suitable for treating gastrointestinal infections, including ones that pose major socioeconomic threats because of their resistance against multiple antibiotics including carbapenems. Hence, an efficient, large-scale method to produce a wide range of antibacterial cyclic peptides is needed but has not yet been developed.

In nature, AE ligases are a family of enzymes that are capable of mediating cyclisation of linear peptides with high catalytic efficiency. However, catalytically active AE ligases often cannot be produced under regular fermenting conditions. Such a technical issue strongly hampers the use of AE ligases as tools for peptide/protein cyclisation.

The prime research goal of this PhD programme is to employ AE ligase as the central catalyst and develop gram-scale biosynthetic procedures of cyclic peptidyl antibacterial reagents. The programme can be dissected into the following objectives:

1.preparing catalytically active AE ligase via specialised fermentation techniques.
2.producing novel cyclic peptides with non-canonical/unnatural amino acids. A combined computational and experimental approach will be used to broaden the recognition sequence in the active site of AE ligase.
3.synthesising cyclic cationic peptides and cell-wall degrading enzymes (e.g. cyclic β-defensin, lysozyme) via whole cell biocatalysis. The stability of the newly prepared cyclic peptidyl reagents will be examined.
4.examining the antibacterial properties of the newly prepared cyclic peptides with principally but not exclusively clinical isolates of multi-drug resistant Escherichia coli and Klebsiella pneumoniae, both of which are listed as major threats in the most recent O’Neil’s Tackling Drug-resistant Infections Globally report.

This PhD programme is an exciting opportunity to help address the current and global crisis of antibiotic resistance. You will be trained over a broad range of techniques, including peptide synthesis, protein production, antibiotic high-throughput screening, computational docking/simulation and protein engineering, all of which are frequently used in the areas of medicinal chemistry, drug discovery and biocatalysis.

Academic criteria

We welcome applications from non-medical backgrounds, especially in areas of computing, mathematics and the physical sciences, and can fund additional training, including master’s degrees to assist discipline conversion.

You must have obtained, or be about to obtain, a 1st or 2:1 UK honours degree, or the equivalent qualification gained outside the UK, in an area appropriate to the skills requirements of the project.

You will also be considered if you have a 2:2 UK honours degree and a master’s degree or have significant relevant non-academic experience.

This research project is in competition with 71 other studentship projects available across the GW4 BioMed MRC Doctoral Training Partnership. Up to 19 studentships will be awarded to the best applicants. http://www.gw4biomed.ac.uk/

Supervisor Dr Louis Luk http://www.cardiff.ac.uk/people/view/122378-luk-louis

Start date 1st October 2018

Deadline for applications 24th November 2017