The development of small peptide-based therapeutics can be accelerated by the knowledge of relationships between the peptide structure and its functional interactions. Here, we report the analysis of two groups of synthetic peptides designed for two applications – broad bactericidal action and inhibition of protein-protein interactions in human cells. Novel amphiphilic peptides designed for antibacterial application incorporated arginine as cationic amino acids and non-natural amino acids that have aromatic side chains with similar hydrophobic properties as tryptophan. The interaction of lead cyclic peptides and their linear analogs with a phospholipid bilayer mimicking a bacterial membrane was studied using nuclear magnetic resonance (NMR) spectroscopy. These results provided insight into the mechanism of peptide bactericidal action and the role of the peptide structure in their activity. In the second example, we perform a structural characterization of a peptide designed to modulate the activation of the NF-kappaB signaling pathway. The peptide was designed to mimic the spatial structure of the HOIP-NZF1 domain interacting with the NEMO CC2-LZ domain to suppress the NF-kappaB activation. The structure elucidation of the designed peptide provided vital information about matching the required pharmacophore structure in the peptide.
","abstract_html":"<p>The development of small peptide-based therapeutics can be accelerated by the knowledge of relationships between the peptide structure and its functional interactions. Here, we report the analysis of two groups of synthetic peptides designed for two applications – broad bactericidal action and inhibition of protein-protein interactions in human cells. Novel amphiphilic peptides designed for antibacterial application incorporated arginine as cationic amino acids and non-natural amino acids that have aromatic side chains with similar hydrophobic properties as tryptophan. The interaction of lead cyclic peptides and their linear analogs with a phospholipid bilayer mimicking a bacterial membrane was studied using nuclear magnetic resonance (NMR) spectroscopy. These results provided insight into the mechanism of peptide bactericidal action and the role of the peptide structure in their activity. In the second example, we perform a structural characterization of a peptide designed to modulate the activation of the NF-kappaB signaling pathway. The peptide was designed to mimic the spatial structure of the HOIP-NZF1 domain interacting with the NEMO CC2-LZ domain to suppress the NF-kappaB activation. The structure elucidation of the designed peptide provided vital information about matching the required pharmacophore structure in the peptide.</p>","abstract_has_math":false,"creators":["Choi, Wonsuk"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Thesis","degree_discipline":"Pharmaceutical Sciences","degree_department":null,"school":null,"contributors":["Dr. Innokentiy Maslennikov","Dr. Simin Rahighi","Dr. Rennolds Ostrom"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2023,"date_issued":"2023-12-01T08:00:00Z","date_published":"2023-12-01T08:00:00Z","updated_at":"2026-07-24T01:38:31Z","subjects":["Structural Biology","NMR Spectroscopy","Amphiphilic Peptides","NF-kB Signaling Pathway","Structure-Based Drug Design","Medicinal and Pharmaceutical Chemistry","Other Biochemistry, Biophysics, and Structural Biology","Other Pharmacy and Pharmaceutical Sciences","Pharmaceutical Preparations","Pharmaceutics and Drug Design"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.chapman.edu/pharmaceutical_sciences_theses/33","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Dr. Innokentiy Maslennikov","Dr. Simin Rahighi","Dr. Rennolds Ostrom"]},{"key":"dc:creator","label":"Author","values":["Choi, Wonsuk"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Pharmaceutical Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Structural Biology","NMR Spectroscopy","Amphiphilic Peptides","NF-kB Signaling Pathway","Structure-Based Drug Design","Medicinal and Pharmaceutical Chemistry","Other Biochemistry, Biophysics, and Structural Biology","Other Pharmacy and Pharmaceutical Sciences","Pharmaceutical Preparations","Pharmaceutics and Drug Design"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.chapman.edu/pharmaceutical_sciences_theses/33"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The development of small peptide-based therapeutics can be accelerated by the knowledge of relationships between the peptide structure and its functional interactions. Here, we report the analysis of two groups of synthetic peptides designed for two applications – broad bactericidal action and inhibition of protein-protein interactions in human cells. Novel amphiphilic peptides designed for antibacterial application incorporated arginine as cationic amino acids and non-natural amino acids that have aromatic side chains with similar hydrophobic properties as tryptophan. The interaction of lead cyclic peptides and their linear analogs with a phospholipid bilayer mimicking a bacterial membrane was studied using nuclear magnetic resonance (NMR) spectroscopy. These results provided insight into the mechanism of peptide bactericidal action and the role of the peptide structure in their activity. In the second example, we perform a structural characterization of a peptide designed to modulate the activation of the NF-kappaB signaling pathway. The peptide was designed to mimic the spatial structure of the HOIP-NZF1 domain interacting with the NEMO CC2-LZ domain to suppress the NF-kappaB activation. The structure elucidation of the designed peptide provided vital information about matching the required pharmacophore structure in the peptide.
"]},{"key":"dc:source","label":"Dc Source","values":["Choi, W. Analyzing Functional Interactions of Designed Peptides by NMR Spectroscopy. [master’s thesis]. Irvine, CA: Chapman University; 2023. https://doi.org/10.36837/chapman.000507"]},{"key":"dc:title","label":"Title","values":["Analyzing Functional Interactions of Designed Peptides by NMR Spectroscopy"]}]}],"canonical_facts":{"dc:contributor":["Dr. Innokentiy Maslennikov","Dr. Simin Rahighi","Dr. Rennolds Ostrom"],"dc:creator":["Choi, Wonsuk"],"dc:description.abstract":["The development of small peptide-based therapeutics can be accelerated by the knowledge of relationships between the peptide structure and its functional interactions. Here, we report the analysis of two groups of synthetic peptides designed for two applications – broad bactericidal action and inhibition of protein-protein interactions in human cells. Novel amphiphilic peptides designed for antibacterial application incorporated arginine as cationic amino acids and non-natural amino acids that have aromatic side chains with similar hydrophobic properties as tryptophan. The interaction of lead cyclic peptides and their linear analogs with a phospholipid bilayer mimicking a bacterial membrane was studied using nuclear magnetic resonance (NMR) spectroscopy. These results provided insight into the mechanism of peptide bactericidal action and the role of the peptide structure in their activity. In the second example, we perform a structural characterization of a peptide designed to modulate the activation of the NF-kappaB signaling pathway. The peptide was designed to mimic the spatial structure of the HOIP-NZF1 domain interacting with the NEMO CC2-LZ domain to suppress the NF-kappaB activation. The structure elucidation of the designed peptide provided vital information about matching the required pharmacophore structure in the peptide.
"],"dc:identifier":["https://digitalcommons.chapman.edu/pharmaceutical_sciences_theses/33"],"dc:source":["Choi, W. Analyzing Functional Interactions of Designed Peptides by NMR Spectroscopy. [master’s thesis]. Irvine, CA: Chapman University; 2023. https://doi.org/10.36837/chapman.000507"],"dc:subject":["Structural Biology","NMR Spectroscopy","Amphiphilic Peptides","NF-kB Signaling Pathway","Structure-Based Drug Design","Medicinal and Pharmaceutical Chemistry","Other Biochemistry, Biophysics, and Structural Biology","Other Pharmacy and Pharmaceutical Sciences","Pharmaceutical Preparations","Pharmaceutics and Drug Design"],"dc:title":["Analyzing Functional Interactions of Designed Peptides by NMR Spectroscopy"],"thesis:degree_discipline":["Pharmaceutical Sciences"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T01:38:31Z"}