Developing Peptide-Based Receptors to Study Molecular Recognition in Water

Abstract

My graduate research career has focused on studying the principles that underlie molecular recognition, which include protein folding, protein-membrane interactions, structural preoranization for target binding and non-covalent interactions. This thesis will present an overview of this work through three different projects. I) Synthetic receptors for target binding in water. Molecular interactions in water provide the foundation for life. More specifically, the interactions between one or more molecules, through hydrogen bonding, π-effects, hydrophobic interactions and electrostatic interactions, all play a significant role essential to biological processes. This chapter will present an overview of supramolecular chemistry in water, with a focus on small molecule receptor “warheads” that target biomolecules of interest. The discussion will then move towards the ability to preorganize these “warheads” on a scaffold to improve their potency towards a target. The fundamental principles discussed in this section will provide a foundation for the following chapter in this thesis.II) Understanding Phosphatidylserine Recognition Using the Model cLac Peptide. The plasma membrane serves as a defining feature of the cell membrane, acting as a barrier for material exchange between a cell and its local environment. More importantly, membrane lipids are involved in mediating numerous cell-signaling events and acting as receptors to recruit proteins that carry out a specific function. Due to the important role that lipids play, it is highly desirable to develop affinity ligands for the diverse range of lipid headgroup structures on a cell membrane. Although prevalent, proteins have intrinsic limitations due to their size, low stabilities and slow clearance rates. This chapter will focus on the model peptide, cLac, which was previously developed as an affinity ligand for phosphatidylserine recognition. We will focus on understanding the key properties that contribute to PS selectivity and affinity, then attempt to improve this scaffold through structural preorganization. III) A prolinomycin-based scaffold for developing functional peptides. Nature has evolved proteins to bind cell-signaling molecules with exquisite affinity and specificity, making molecular recognition an essential part of biology. It has been a highly sought after goal within the chemistry field to be able to mimic the structure and function of certain proteins with smaller molecules, such as peptides. Specifically, cyclic peptides are showing promise as therapeutic agents due to their high proteolytic stabilities, faster clearance rates and ease of synthesis compared to proteins. One challenge, however, is that peptides generally do not possess the ability to properly fold and display their side chains for target binding, as proteins do. In this chapter, I will present a prolinomycin-based scaffold, which can fold in the presence of K+ ions to preorganize its side chains for target binding. Moreover, the focus will be on the structural aspects of this cyclic peptide, along with proof-of-concept studies demonstrating its ability to recognize a target under physiological conditions. The findings in this study will be useful in developing peptide-based tools that recognize various targets. IV) Dissecting the energetic consequences of fluorinating a protein core. Proteins have emerged as a powerful class of therapeutic agents due to their superior properties over small molecules in the clinic. Some of the key advantages include their large surface areas and highly defined structures, which allow them to perform very specific functions that are generally not reproducible with traditional small molecule scaffolds. In addition, proteins possess the ability to properly fold under physiological conditions through precise, noncovalent interactions between their side chain residues. Perhaps the most relevant interactions arise from aromatic side chains, which can interact in a variety of ways to help proteins fold. In this chapter, we will focus on the model protein, VHP35, which contains a hydrophobic core of three interacting Phe residues, to study the effects of fluorination on an edge-face interaction.