Capsules with character: building a new generation of macrocyclic receptors targeting post-translational modifications

A joint Crick-King's College London funded PhD position for the 2022 programme between the labs of Charlie McTernan and Manuel Müller.

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Applications for the 2022 PhD programme are now open until 12:00 noon GMT, Thursday 11 November 2021.

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Project background and description

 

Supramolecular chemistry is often inspired by the functionality and complexity of nature. Enzymes are capable of recognising, and transforming, specific targets in an immensely complex and crowded milieu [1]. Whilst great strides have been made towards achieving artificial analogues of these biological guest binders, with an array of simple macrocycles and capsules reported [2], synthetic systems have been unable to match the specificity vital to the processes of biology [3]. This project seeks to remedy this by combining the defined, three-dimensional macrocyclic cavities built by supramolecular chemists with the information-rich polymers of biology – here, peptides.

This combination will allow us to improve the solubility of macrocycles in water, by including charged amino acids, and to design diverse cavities for targeted binding, which will act as minimal, small-molecule mimics of biological receptors. As such, we will combine the best aspects of both synthetic and biological interaction modes – the specificity of biological systems, with the small size, easy synthesis, and potential to pass cell membranes of synthetic systems.

This project will develop strong and specific binders of an array of biologically critical post-translational modifications. We will initially target phosphorylation, and in particular, phosphorylation of p53, whose function as a critical tumour suppressor protein is controlled by an array of post-translational modifications. The Müller lab are experts in the effect of post-translational modifications on p53 [4], and the McTernan group are expert in the synthesis of supramolecular architectures [5].

The novelty in this work is two-fold – targeting non-cationic post-translational modifications and those beyond methylation; and gaining a degree of specificity for certain proteins. Initial work will be based in the McTernan group, generating an array of amino-acid functionalised (bearing c. 10 sets of chains/loops of 3-7 amino acids) macrocyclic compounds (including pillararenes and bambusurils), and optimising their binding for isolated amino acids bearing post-translational modifications (such as phosphoserine, phosphotyrosine, or acetyllysine). Once the key design parameters have been established, and strong and selective binding achieved, work will move to use the skills of the Müller lab in peptide and protein synthesis and semi-synthesis, to investigate the recognition of post-translationally modified residues in the context of larger peptides and then entire proteins. In particular, we will evaluate the ability of designed capsules to distinguish patterns of phosphorylation (through bivalent binding) and even sequence context (through secondary contacts). This will be a collaborative and iterative process, with results from protein binding feeding back to the design of new, more selective, macrocyclic probes.

The successful candidate will gain skills in supramolecular chemistry, host-guest design and optimisation, protein expression and semi-synthesis, and biochemical assays. They will become expert in NMR interpretation, organic synthesis, mass spectrometry, protein expression and semi-synthesis, ITC measurements, and peptide synthesis.

By creating new ways to monitor post-translational modifications, we will facilitate a deeper understanding of these fascinating transformations and the potential to selectively manipulate aberrant phosphorylation-driven signalling processes.

Diagram showing supramolecular molecules

Candidate background

 

This project would suit candidates with a background in chemistry or biochemistry, and an interest in working at the interface between disciplines. An interest in organic synthesis would be an asset, as would a willingness to learn new techniques.

References

 

1.         Gao, M. and Skolnick, J. (2013)

            A comprehensive survey of small-molecule binding pockets in proteins.

            PLOS Computational Biology 9: e1003302. PubMed abstract

2.         Erbas-Cakmak, S., Leigh, D.A., McTernan, C.T. and Nussbaumer, A.L. (2015)

            Artificial molecular machines.

            Chemical Reviews 115: 10081-10206.

3.         Dong, J. and Davis, A.P. (2021)

            Molecular recognition mediated by hydrogen bonding in aqueous media.

            Angewandte Chemie International Edition 60: 8035-8048. PubMed abstract

4.         Margiola, S., Gerecht, K. and Müller, M.M. (2021)

            Semisynthetic ‘designer’ p53 sheds light on a phosphorylation-acetylation relay.

            Chemical Science 12: 8563-8570.

5.         McTernan, C.T., Ronson, T.K. and Nitschke, J.R. (2019)

            Post-assembly modification of phosphine cages controls host-guest behavior.

            Journal of the American Chemical Society 141: 6837-6842. PubMed abstract