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Peptide-derived macrocycles are a potentially rich source of biologically active lead structures, which are capable of recapitulating a therapeutic protein-protein surface interaction. Their three-dimensional shape influences both the macrocycle’s binding to protein surfaces as well as its pharmacological properties. While other cyclization methods have focused on ring formation to yield singular products from a given peptide, small template molecules can also be used as hydrophobic scaffolds to engage and cyclize unprotected peptides in order access regioisomeric variants of each peptide sequence. In this way, we hope to engineer improved pharmacological and therapeutic properties of bioactive or bio-inspired peptides. These designed template molecules incrementally constrain peptide structure through systematic cyclizations to restrict conformation and stabilize against degradation by metabolic enzymes. These hybrid molecules are intended to retain molecular recognition elements in the biopolymer while displaying that functionality as part of stable polycycles having defined shapes and improved pharmacological properties. Chapter 2 covers Friedel-Crafts macrocinnamylations of tryptophan-containing peptides, specifically studying the endo-pyrroloindoline products produced from such reactions. We found this product to be sensitive to acidic conditions, which lead to regioisomeric rearrangement products. We studied the kinetics of this rearrangement both experimentally and computationally.In Chapter 3, the synthesis and use of a new, four-armed template molecule, which now bears a terminal alkyne are detailed. We utilized the terminal alkyne as a site for glycosylation through a copper-catalyzed Huisgen cycloaddition as well as a dimerization event. This now third generation template afforded regioisomeric macrocyclic products derived from the second mitochondrial activator of caspases (Smac) N-terminus, which displayed differing affinities for inhibitor of apoptosis proteins (IAPs). In Chapter 4, methods to engage the terminal alkyne of the third generation template in a unimolecular reaction are investigated. Although a bicyclization reaction eluded us, the data discussed therein may provide insight into further endeavors.