Developing functional peptides as synthetic receptors, binders of protein and probes for bacteria detection

Abstract

Nature has developed a generous number of peptides carrying out various essential functions in all living organisms. Human body produces peptides as signaling molecules, such as hormones, to transmit messages from cell to cell and regulate metabolic homeostasis. Microbes synthesize peptides as antibiotics to inhibit the growth of other microorganisms. These peptides display an exceeding diversity of amino acid composition, peptide sequence, secondary structure and post-translational modification. Inspired by nature, researchers have developed peptides as a unique modality of therapeutics, combining the best attributes of small-molecule drugs and protein-based biopharmaceuticals. This work has sought to explore the potential of peptides as synthetic receptors, binders of protein and probes for bacteria detection. The research started from a foldable cyclic peptide scaffold, prolinomycin, a proline-rich analogue of valinomycin. The peptide can chelate a potassium ion folding into a drum like structure, which provides a platform to display and preoganize functional side chains for target binding. We first investigated its folding behavior under physiological conditions. We demonstrate that the metal-assisted folding of the prolinomycin scaffold tolerates various side chain mutations. The stability of the structure can be improved by introducing crosslinking moieties. Based on this scaffold, we rationally designed synthetic receptors of various amines by utilizing iminoboronate chemistry with acetylphenyl boronic acid (APBA). Furthermore, I pursued phage display, a powerful technique to develop high affinity peptide binders of protein targets. Proteins are the most appealing targets for drug development and disease biomarkers discovery. We chose sortase A (SrtA) as a model target protein to screen for potent peptide binders. A peptide inhibitor of sortase A with single-digit micromolar affinity was identified from a cyclic peptide library displayed by phage. In addition, from the chemically modified phage display peptide library presenting APBA motifs, peptide binders with specificity and micromolar affinity towards SrtA were discovered. Instead of binding to the active site, the peptide could recognize the surface of the protein. Additionally, to further expand the chemical space of phage display, I constructed a phage display peptide library presenting N-terminal cysteine (NCys) which can undergo site-specific chemical modifications. Two pieces of chemistry were applied, including thiazolidino boronate (Tzb) mediated acylation reaction of NCys and 2-cyanobenzothiazole (CBT)-NCys condensation. The site-specific dual modifications on NCys and internal Cys of phage-encoded peptides were achieved. Furthermore, a strategy to N, S-doubly label NCys via an alternative pathway of CBT condensation was reported, which presents a significant addition to the toolbox for site-specific protein modifications. Finally, by functionalizing graphene field effect transistors (G-FET) with peptide probes, we developed the first selective, electrical detection of the pathogenic bacterial species Staphylococcus aureus and antibiotic resistant Acinetobacter baumannii on a single platform. Overall, peptides provide enormous opportunities for therapeutics development. Research herein demonstrated principles of peptide design for specific molecular recognition. Novel chemistry strategies have been developed to expand the molecular diversity of peptide libraries. We believed that the advances in peptide design and screening would promote peptide-based drug discovery.