Development of Peptidomimetic Tools to Understand and Modulate the Function of Bacterial Outer Membrane Proteins University of Birmingham in United Kingdom

The rise of antibiotic-resistant bacteria poses a significant and escalating global threat, demanding new approaches and targets to fight infections. This issue is particularly critical with Gram-negative bacteria, as there are very few antibiotics in development, and new options for clinical use are unlikely to emerge soon. Gram-negative bacteria are generally more resistant to antibiotics than Gram-positive bacteria due to their complex cell envelope structure, which includes an additional outer membrane (OM). This outer membrane has a unique lipid arrangement, with lipopolysaccharides (LPS) on the outer layer and phospholipids on the inner layer, providing enhanced protection. It acts as a barrier to hydrophilic molecules and slows the penetration of small hydrophobic molecules, contributing to their higher resistance to hydrophobic antibiotics and detergents. The proteins embedded in the outer membrane are central to microbial defense, playing critical roles in pathogenesis, virulence, and multidrug resistance. These outer membrane proteins (OMPs) are involved in key processes driving infection and disease progression, and they are vital for maintaining cellular homeostasis by allowing the excretion of toxic substances, like antibiotics, and the uptake of nutrients. Given the outer membrane's importance, understanding its biogenesis is essential both as a fundamental biological process and as a potential avenue for developing new antibiotic targets.

The Maintenance of outer membrane Lipid Asymmetry (Mla) pathway is a multicomponent system found in all gram-negative bacteria that contributes to virulence, vesicle blebbing and preservation of the outer membrane barrier function. It acts by maintaining outer membrane asymmetry by removing ectopic lipids from the outer leaflet of the outer membrane and returning them to the inner membrane through three proteinaceous assemblies. The MlaA-OmpC complex, situated within the outer membrane; the periplasmic phospholipid shuttle protein, MlaC; and the inner membrane ABC transporter complex, MlaFEDB. Building on our expertise in developing peptidomimetic inhibitors of protein-protein interactions (Fig. 1)1-3 this project focuses on developing candidate ligands that mimic (i) the OM lipoprotein MlaA and potentiate its interaction with OmpC.4 (ii) the OM lipoproteins MlaC and MlaD to inhibit their protein-protein interactions.5 This will be complemented by development of chemical probes of these peptidomimetics for phospholipid binding that can exploit the rapid and non-specific labelling of diazirines.6

Such reagents will allow us to assess the consequence of protein-protein interaction inhibition on ligand binding and localization. Collectively these chemical probes will represent unique tools to modulate protein-protein interactions involved in OM biogenesis allowing us to understand their functional role and provide starting points for development of new antimicrobial mitigations. You will join a vibrant, diverse and group of researchers to gain skills and knowledge in chemical biology in its broadest sense, and, participate in our wider collaborative research.

Specific techniques include:

This project will develop multidisciplinary skills in synthetic chemistry, structural molecular biology and cell biology; it will harness cutting edge data analyses tools (incl. R, Relion, CryoSparc, CCP4, alphafold etc), giving the student computational and quantitative bioscience capabilities.

Eligibility:

Entry requirements: The candidate should normally have, or expect to receive, a first or upper second (2.1) class Masters degree (or equivalent). The interdisciplinary nature of this research means that we welcome applications from students with backgrounds in any biological, chemical, and/or physical science, who are interested in using their skills in addressing biological questions. Please contact Prof Andy Wilson ( [email protected] ) Dr Tim Knowles ( [email protected] ) for further details about this project. For more information on our group’s current research activity see: https://ajwilsonresearch.com/

English language requirements: The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent (e.g. TOEFL, PTE etc.). The test must be dated within two years of the start date of the course in order to be valid.

References:

1. R. S. Dawber, D. Gimenez, M. Batchelor, J. A. Miles, M. H. Wright, R. Bayliss and A. J. Wilson, ChemBioChem, 2024, 25, e202300649.

2. E. E. Cawood, E. Baker, T. A. Edwards, D. N. Woolfson, T. K. Karamanos and A. J. Wilson, Chem. Sci., 2024, DOI: 10.1039/D4SC02240H.

3. F. Hóbor, Z. Hegedüs, A. A. Ibarra, V. L. Petrovicz, G. J. Bartlett, R. B. Sessions, A. J. Wilson and T. A. Edwards, RSC. Chem. Biol., 2022, 3, 592-603.

4. J. Abellón-Ruiz, S. S. Kaptan, A. Baslé, B. Claudi, D. Bumann, U. Kleinekathöfer and B. van den Berg, Nature Microbiology, 2017, 2, 1616-1623.

5. P. Wotherspoon, H. Johnston, D. J. Hardy, R. Holyfield, S. Bui, G. Ratkeviciute, P. Sridhar, J. Colburn, C. B. Wilson, A. Colyer, B. F. Cooper, J. A. Bryant, G. W. Hughes, P. J. Stansfeld, J. R. C. Bergeron and T. J. Knowles, Nat. Commun., 2024, 15, 6394.

6. J. E. Horne, M. Walko, A. N. Calabrese, M. A. Levenstein, D. J. Brockwell, N. Kapur, A. J. Wilson and S. E. Radford, Angew. Chem. Int. Ed., 2018, 57, 16688-16692.