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Peptidoglycan is a key component of the bacterial cell wall and is an essential structure for protecting the cell from lysis due to high osmotic pressure. Because of its importance, peptidoglycan has become a prominent target for antibiotic design as well as a number of host defense mechanisms. In response, many bacteria have developed methods of evading or minimizing the effects of these antibiotics and defense mechanisms through the modification of their peptidoglycan. One such modification, found in a number of bacterial species, is the O-acetylation of N-acetylmuramic acid (MurNAc) residues of peptidoglycan. This modification decreases the hydrolytic activity of lysozyme, an enzyme that is released as a response to bacterial infection, on peptidoglycan, and results in increased bacterial pathogenicity and virulence. The enzyme O-acetylpeptidoglycan esterase (Ape1) from Neisseria gonorrhoeae is an important enzyme involved in the bacterial O-acetylation/deacetylation pathway, and has been shown to be essential for bacterial viability. In this thesis, we detail the design and testing of water-soluble monosaccharide and disaccharide substrates of Ape1 (compounds 1 and 2) and preliminary work towards the design and testing of small-molecule inhibitors of the enzyme. Disaccharide 1 and monosaccharide 2 both served as substrates of Ape1, indicating that a polymeric substrate is not required for efficient catalysis. Our monosaccharide scaffold was chosen for the design of future generations of inhibitors. The enzyme N-acetylmuramic acid 6-phosphate hydrolase (MurQ) is essential for the recycling of MurNAc residues in peptidoglycan. This recycling process serves to reincorporate cell wall components into synthetic precursors that can be used in peptidoglycan biosynthesis as well as other basic metabolic pathways. MurQ catalyzes the conversion of MurNAc 6-phosphate to GlcNAc 6-phosphate through cleavage of a lactyl ether. In this thesis, studies on the mechanism through which MurQ catalyzes hydrolysis of the lactyl ether of MurNAc 6-phosphate are reported. By probing the reaction with chemically synthesized substrate and substrate analogues, an E1cB-like mechanism with an (E)-alkene intermediate is proposed. The amino acids Glu83 and Glu114 are implicated as important residues in catalysis, and their specific roles are also explored in the context of our proposed mechanism.