Date of Award

Fall 12-18-2018

Degree Type

Dissertation

Degree Name

PhD. Chemistry

Department

Chemistry and Biochemistry

Advisor

David Sabatino, Ph.D.

Committee Member

Monika Raj, Ph.D.

Committee Member

Cecilia Marzabadi, Ph.D.

Committee Member

Stephen Kelty, Ph.D.

Keywords

glutamic acid, stapling, lysine, carbonylating agent, site-selective cleavage

Abstract

While natural peptides, are ideal starting points for peptide-based drug design and development, they suffer from high conformational instability, which results in susceptibility to proteolytic degradation and poor bioavailability. Peptidomimetics in recent years has helped circumvent these shortcomings by improving the pharmacological properties of polypeptides. Peptidomimetics contain essential elements (pharmacophores) that mimic a natural peptide or protein in 3D space and retain the ability to interact with the biological target producing the same biological effect. In contrast, they offer conformationally restricted structures, potentially minimizing cross-target interactions, which leads to better transport properties through biologic membranes and resistance to immune responses.

Over the years, a wide variety of side chain modified polypeptides have been developed. These modifications have been found to affect both functional as well as conformational properties of polypeptides. This important application has proven to be the motivating force behind the two research projects described in this thesis.

The site selective cleavage of peptide bonds is an essential complementary tool in protein sequencing and various bioanalytical and biotherapeutic applications of peptides and proteins.In order to cleave unreactive peptide bonds, mild and metal free, a glutamic acid selective cleavage methodology with a broad substrate scope has been developed as reported in Chapter 2 of this thesis. This methodology involves activation of side-chain carboxylate groups of glutamic acid residues followed by nucleophilic attack of the backbone amide nitrogen resulting in the formation of a cyclic pyroglutamate imide intermediate. The latter renders the scissile peptide bond susceptible to cleavage under neutral aqueous conditions. Most importantly, the strategy provides an efficient tool for peptidolysis in a wide range of peptide sequences, including Pro-Glu, disulfide bonding sites and at unnatural amino acid residues such as D-amino acids in mutated peptides. The latter provides a chemical tool for cleaving peptidomimetics that are unsuitable substrates for proteases and may be potentially applicable for determining the mutations responsible for various age-related disorders.

Though conformational instability of peptides resulting in reduced bioavailability limits their use as promising drugs, constraining peptides by stapling (or cyclizing the side chain components in peptides) improves their pharmacological performance by imparting structural stability and increased bioavailability. In this regard, a biocompatible, mild and metal free stapling methodology with a broad substrate scope is reported in Chapter 3 of this thesis. In this method, the nucleophilic side chain of lysine is modified by reaction with an electrophilic bifunctional carbonylating agent to form urea stapled peptides with increased α-helicity and improved proteolytic stability. Additionally, the stapling strategy demonstrated the ability to synthesize bicyclic peptides with potential applications in peptide-based drug design. Most importantly, the urea moiety is anticipated to form strong H-bonds, which may be useful in catalyzing organic asymmetric transformations.

In summary, the research reported in this thesis describes design, development of peptidomimetics through side-chain modifications of glutamic acid and lysine residues and their significant potential applications in peptide based synthetic chemistry and drug design.

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