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A Phage Display Approach to Identify Targeted Covalent Inhibitors for ‘Undruggable’ Proteins


   Department of Life Sciences

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  Dr Scott Lovell, Prof Jody Mason, Prof Jean van den Elsen  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

The University of Bath is inviting applications for the following funded PhD project commencing in October 2022.

Background:

During the past decade, covalent targeting has experienced a resurgence. So-called “targeted covalent inhibitors” (TCIs), which modify poorly conserved non-catalytic amino acids on proteins, now provide the basis for a multitude of industrial drug discovery programs. TCIs offer advantages compared to reversible ligands including non-equilibrium kinetics, full target occupancy and a decoupling of pharmacodynamics from pharmacokinetics.1 TCIs are typically generated by modifying optimised reversible ligands with a latent electrophile.2 Consequently, despite their useful properties TCIs only exist for a small number of protein targets and the TCI research field would greatly benefit from an unbiased screening method to identify new classes of TCIs from diverse pools of candidate molecules. Recently, we have reported a phage display approach to screen for potent and selective mechanism-based covalent inhibitors of cysteine and serine hydrolases.This approach, which uses a reactive linker to form cyclic peptides on the phage surface while simultaneously introducing an electrophile to covalently react with the active site nucleophile, allows screening of billions of covalent cyclic peptides against a target hydrolase.

Project Outline:

In this PhD project, you will adapt the phage technology to enable de novo identification of targeted covalent cyclic peptides (TCCPs) for proteins currently deemed undruggable. Key to this idea is the identification of a cyclic peptide that perfectly positions a latent electrophile in proximity to a non-catalytic and non-conserved nucleophilic residue enabling highly selective covalent modification of the protein target. As a proof-of-principle of the technology you will develop TCCPs that selectivity inhibit PD-L1. Blockade of the PD-L1/PD-1 axis is considered a major strategy to overcome immune resistance in various cancers by reactivating the T cell response. Previously, genetic code expansion has been used to introduce fluorosulfate-L-tyrosine (FSY), a latent electrophilic amino acid, into a single position (Ala129 to FSY129) in PD-1. This resulted in selective irreversible binding to PD-L1 in vivo through covalent modification of a proximal His residue4. Building on this finding, you will incorporate fluorosulfate fragments into various phage display libraries to generate billions of covalent macrocycles to screen against PD-L1. The binding mode of any hit TCCPs will be identified using a combination of chemical proteomics and x-ray crystallography. Next, you will construct a library of electrophilic fragments to target diverse amino acid residues5 and develop a standardized protocol and pipeline, which will combine TCCP phage library screens with bioinformatic and chemoproteomic analyses, to enable discovery of covalent ligands for any protein target in less than 4 weeks.

Training Opportunities:

This is a multi-disciplinary project in the broad research field of chemical biology. The successful candidate will receive hands-on training in organic synthesis, peptide chemistry, molecular biology, cloning, phage display, chemical proteomics, reactivity-based protein profiling, analysis of NGS datasets and structural biology.

Project keywords: Covalent Inhibitors, Drug Discovery, Chemical Proteomics, Phage Display, Undruggable Proteins

Candidate Requirements:

It is expected that the successful candidate:

  • will hold, or expect to receive, a Master's level degree or an excellent/First Class Bachelor's degree with Honours (or equivalent) in Chemistry, Biochemistry or a closely related discipline;
  • will possess a keen interest in drug discovery and using chemistry and chemical biology to address unmet needs in health and disease;
  • may have experience of molecular cloning and/or analysis of NGS datasets (desirable but not essential).

Non-UK applicants must meet our English language entry requirement.

The successful student will be expected to complete annual progress reports and make a copy of their thesis available to the studentship funder, Applied Molecular Transport (AMT), upon its completion.

Enquiries and Applications:

Informal enquiries are welcomed and may be directed to Dr Scott Lovell [Email Address Removed].

Formal applications should be made via the University of Bath’s online application form for a PhD in Biochemistry.

More information about applying for a PhD at Bath may be found on our website.

Funding Eligibility:

To be eligible for funding, you must qualify as a Home student. The eligibility criteria for Home fee status are detailed and too complex to be summarised here in full; however, as a general guide, the following applicants will normally qualify subject to meeting residency requirements: UK nationals (living in the UK or EEA/Switzerland), Irish nationals (living in the UK or EEA/Switzerland), those with Indefinite Leave to Remain and EU nationals with pre-settled or settled status in the UK under the EU Settlement Scheme). This is not intended to be an exhaustive list. Additional information may be found on our fee status guidance webpage, on the GOV.UK website and on the UKCISA website.

Exceptional Overseas students (e.g. with a UK Master’s Distinction or international equivalent and relevant research experience), who are interested in this project, should contact the lead supervisor in the first instance to discuss the possibility of applying for supplementary funding.

Equality, Diversity and Inclusion:

We value a diverse research environment and aim to be an inclusive university, where difference is celebrated and respected. We welcome and encourage applications from under-represented groups.

If you have circumstances that you feel we should be aware of that have affected your educational attainment, then please feel free to tell us about it in your application form. The best way to do this is a short paragraph at the end of your personal statement.


Funding Notes

The successful candidate will receive a 3-year studentship funded by Applied Molecular Transport (AMT). The funding will cover Home tuition fees and will provide a stipend at the UKRI rate (£15,609 per annum, 2021/22 rate) along with a budget for research/training expenses. Eligibility criteria apply – see Funding Eligibility section above.

References

1. Gehringer, M., & Laufer, S. A. (2019). Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. Journal of Medicinal Chemistry, 62(12), 5673–5724.
2. Ippolito, J. A., Niu, H., Bertoletti, N., Carter, Z. J., Jin, S., Spasov, K. A., Cisneros, J. A., Valhondo, M., Cutrona, K. J., Anderson, K. S., & Jorgensen, W. L. (2021). Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead. ACS Medicinal Chemistry Letters, 12(2), 249–255.
3. Chen, S., Lovell, S., Lee, S., Fellner, M., Mace, P. D., & Bogyo, M. (2021). Identification of highly selective covalent inhibitors by phage display. Nature Biotechnology, 39(4), 490–498.
4. Li, Q., Chen, Q., Klauser, P. C., Li, M., Zheng, F., Wang, N., Li, X., Zhang, Q., Fu, X., Wang, Q., Xu, Y., & Wang, L. (2020). Developing Covalent Protein Drugs via Proximity-Enabled Reactive Therapeutics. Cell, 182(1), 85-97
5. Zanon, P. R. A., Yu, F., Musacchio, P., Lewald, L., Zollo, M., Krauskopf, K., Mrdović, D., Raunft, P., Maher, T. E., Cigler, M., Chang, C., Lang, K., Toste, F. D., Nesvizhskii, A. I., & Hacker, S. M. (2021). Profiling the Proteome-Wide Selectivity of Diverse Electrophiles. ChemRxiv
6. Lovell, S., Zhang, L., Kryza, T., Neodo, A., Bock, N., Vita, E. De, Williams, E. D., Engelsberger, E., Xu, C., Bakker, A. T., Maneiro, M., Tanaka, R. J., Bevan, C. L., Clements, J. A., & Tate, E. W. (2021). A Suite of Activity-Based Probes To Dissect the KLK Activome in Drug-Resistant Prostate Cancer. Journal of the American Chemical Society, 143(23), 8911–8924.
7. Kryza, T*., Khan, T*., Lovell, S*., Harrington, B. S., Yin, J., Porazinski, S., Pajic, M., Koistinen, H., Rantala, J. K., Dreyer, T., Magdolen, V., Reuning, U., He, Y., Tate, E. W., & Hooper, J. D. (2021). Substrate-biased activity-based probes identify proteases that cleave receptor CDCP1. Nature Chemical Biology 2021 17:7, 17(7), 776–783.
8. Faucher, F., Bennett, J. M., Bogyo, M., & Lovell, S. (2020). Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chemical Biology, 27(8), 937–952.
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