Synthetic Approaches to Protein Functionalisation and Sensing

The use of aptamers, which are oligonucleotides that bind to specific target molecules, also allows for development of diagnostic tools and macromolecular drugs. Typically, aptamers are developed via Systemic Evolution of Ligands by Exponential Enrichment (SELEX) process. SELEX has inherent limitations. The most notable being limited chemical diversity, which strongly influences the interaction between an affinity reagent and its target and directly affects binding affinity and specificity. SELEX relies on enzymatic amplification of an oligonucleotide library, therefore, only nucleotides that are compatible with PCR amplification can be used. In contrast, fragment-based approaches to finding novel small molecules that bind to proteins are well-established in drug discovery. The key concept is that weakly-binding small fragments form high-quality interactions that can be optimised into potent larger molecules with high binding affinities through linking, elaboration or merging strategies. In this context, the ability to selectively functionalise amino acid residues with functional fragments can offer key insights into protein function, allowing for key advances in the fields of drug discovery and sensing. There are a range of established methods allowing for the selective functionalisation of cysteine, lysine, tryptophan and tyrosine residues.
In this research project, it is proposed to take the above concepts and techniques from protein functionalisation and fragment-based drug discovery and apply them to developing molecules with possible applications in sensor development for biomarkers of disease or new technology for drug discovery. The molecules developed for protein functionalisation will be bifunctional, allowing them to be covalently linked to a peptide or protein at one 'end' of the molecule via covalent bonds to targetable residues. An easily functionalised handle at the other end of the molecule will allow for easy coupling with a variety of substrates, for example fluorophores or drug-like molecules.