{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/118259"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/118259","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Peptide-mediated delivery of antisense oligonucleotides and chemotherapeutics across biological barriers","abstract":"Many nucleic acids, peptides, and small molecules struggle to become clinically viable therapeutics as a result of poor delivery. Biological barriers such as the plasma membrane and the blood-brain barrier (BBB) contribute to this challenge as they can limit the passage of macromolecules. Cell-penetrating peptides (CPPs) that interact with membranes can improve the uptake of macromolecules across biological barriers. Here we explore methods for the peptide-mediated delivery of antisense oligonucleotides (ASOs) and chemotherapeutics. First, we address the issue that the optimal peptide sequence for the delivery of a macromolecular cargo is often context-dependent and specific to that cargo. With one class of ASO, we develop a paradigm that combines systematic screening of known CPPs in a functional assay for ASO delivery with machine learning methods. Using our computational model, we identify five novel sequences that increase ASO activity at least three-fold. Next, we demonstrate that combining CPPs of different classes generates chimeric peptides with synergistic effects on ASO delivery. These chimeras improve ASO activity twenty-fold, which is greater than any literature-reported sequence. Then, we examine peptide cyclization with perfluoroaryl-cysteine SNAr chemistry to improve the stability and delivery of peptide-ASO conjugates. We extend our SNAr chemistry to the synthesis of arginine-rich bicyclic peptides, which are more stable to proteolysis than single cycles. Both perfluoroaryl cyclic and bicyclic arginine-rich peptides improve ASO activity fourteen-fold. Consequently, we demonstrate that peptide cyclization with perfluoroaryl-cysteine SNAr chemistry enhances the ability of peptides to cross the BBB. We prepare macrocyclic analogues of both a CPP and a therapeutic peptide. We show that a subset of the macrocycles cross the BBB in both a cellular spheroid model of the BBB, as well as after intravenous injection in mice. Finally, we conjugate a platinum (IV) prodrug of the chemotherapeutic cisplatin to a brain-penetrating perfluoroaryl macrocycle and show that the amount of platinum in the mouse brain is fifteen-fold greater than cisplatin after five hours. In summary, we explore strategies to improve the peptide-mediated delivery of ASOs and small molecule chemotherapeutics across biological barriers. In the future, we envision extending these approaches to other macromolecular cargos of therapeutic interest.","abstract_html":"Many nucleic acids, peptides, and small molecules struggle to become clinically viable therapeutics as a result of poor delivery. Biological barriers such as the plasma membrane and the blood-brain barrier (BBB) contribute to this challenge as they can limit the passage of macromolecules. Cell-penetrating peptides (CPPs) that interact with membranes can improve the uptake of macromolecules across biological barriers. Here we explore methods for the peptide-mediated delivery of antisense oligonucleotides (ASOs) and chemotherapeutics. First, we address the issue that the optimal peptide sequence for the delivery of a macromolecular cargo is often context-dependent and specific to that cargo. With one class of ASO, we develop a paradigm that combines systematic screening of known CPPs in a functional assay for ASO delivery with machine learning methods. Using our computational model, we identify five novel sequences that increase ASO activity at least three-fold. Next, we demonstrate that combining CPPs of different classes generates chimeric peptides with synergistic effects on ASO delivery. These chimeras improve ASO activity twenty-fold, which is greater than any literature-reported sequence. Then, we examine peptide cyclization with perfluoroaryl-cysteine SNAr chemistry to improve the stability and delivery of peptide-ASO conjugates. We extend our SNAr chemistry to the synthesis of arginine-rich bicyclic peptides, which are more stable to proteolysis than single cycles. Both perfluoroaryl cyclic and bicyclic arginine-rich peptides improve ASO activity fourteen-fold. Consequently, we demonstrate that peptide cyclization with perfluoroaryl-cysteine SNAr chemistry enhances the ability of peptides to cross the BBB. We prepare macrocyclic analogues of both a CPP and a therapeutic peptide. We show that a subset of the macrocycles cross the BBB in both a cellular spheroid model of the BBB, as well as after intravenous injection in mice. Finally, we conjugate a platinum (IV) prodrug of the chemotherapeutic cisplatin to a brain-penetrating perfluoroaryl macrocycle and show that the amount of platinum in the mouse brain is fifteen-fold greater than cisplatin after five hours. In summary, we explore strategies to improve the peptide-mediated delivery of ASOs and small molecule chemotherapeutics across biological barriers. In the future, we envision extending these approaches to other macromolecular cargos of therapeutic interest.","abstract_has_math":false,"creators":["Fadzen, Colin MacLaine"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Chemistry.","school":null,"contributors":[],"advisors":["Bradley L. Pentelute."],"committee_chairs":[],"committee_members":[],"year":2018,"date_issued":"2018","date_published":"2018","updated_at":"2026-07-22T22:22:08Z","subjects":["Chemistry."],"languages":["eng"],"rights":["MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1721.1/118259","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Bradley L. Pentelute."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. 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They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1721.1/118259"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis: Ph. D. in Biological Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2018.","Cataloged from PDF version of thesis.","Includes bibliographical references."]},{"key":"dc:description.abstract","label":"Abstract","values":["Many nucleic acids, peptides, and small molecules struggle to become clinically viable therapeutics as a result of poor delivery. Biological barriers such as the plasma membrane and the blood-brain barrier (BBB) contribute to this challenge as they can limit the passage of macromolecules. Cell-penetrating peptides (CPPs) that interact with membranes can improve the uptake of macromolecules across biological barriers. Here we explore methods for the peptide-mediated delivery of antisense oligonucleotides (ASOs) and chemotherapeutics. First, we address the issue that the optimal peptide sequence for the delivery of a macromolecular cargo is often context-dependent and specific to that cargo. With one class of ASO, we develop a paradigm that combines systematic screening of known CPPs in a functional assay for ASO delivery with machine learning methods. Using our computational model, we identify five novel sequences that increase ASO activity at least three-fold. Next, we demonstrate that combining CPPs of different classes generates chimeric peptides with synergistic effects on ASO delivery. These chimeras improve ASO activity twenty-fold, which is greater than any literature-reported sequence. Then, we examine peptide cyclization with perfluoroaryl-cysteine SNAr chemistry to improve the stability and delivery of peptide-ASO conjugates. We extend our SNAr chemistry to the synthesis of arginine-rich bicyclic peptides, which are more stable to proteolysis than single cycles. Both perfluoroaryl cyclic and bicyclic arginine-rich peptides improve ASO activity fourteen-fold. Consequently, we demonstrate that peptide cyclization with perfluoroaryl-cysteine SNAr chemistry enhances the ability of peptides to cross the BBB. We prepare macrocyclic analogues of both a CPP and a therapeutic peptide. We show that a subset of the macrocycles cross the BBB in both a cellular spheroid model of the BBB, as well as after intravenous injection in mice. Finally, we conjugate a platinum (IV) prodrug of the chemotherapeutic cisplatin to a brain-penetrating perfluoroaryl macrocycle and show that the amount of platinum in the mouse brain is fifteen-fold greater than cisplatin after five hours. In summary, we explore strategies to improve the peptide-mediated delivery of ASOs and small molecule chemotherapeutics across biological barriers. In the future, we envision extending these approaches to other macromolecular cargos of therapeutic interest."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph. D. in Biological Chemistry"]},{"key":"dc:title","label":"Title","values":["Peptide-mediated delivery of antisense oligonucleotides and chemotherapeutics across biological barriers"]}]}],"canonical_facts":{"dc:contributor.advisor":["Bradley L. Pentelute."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Chemistry."],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Chemistry."],"dc:creator":["Fadzen, Colin MacLaine"],"dc:date.accessioned":["2018-09-28T20:59:07Z"],"dc:date.available":["2018-09-28T20:59:07Z"],"dc:date.issued":["2018"],"dc:description":["Thesis: Ph. D. in Biological Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2018.","Cataloged from PDF version of thesis.","Includes bibliographical references."],"dc:description.abstract":["Many nucleic acids, peptides, and small molecules struggle to become clinically viable therapeutics as a result of poor delivery. Biological barriers such as the plasma membrane and the blood-brain barrier (BBB) contribute to this challenge as they can limit the passage of macromolecules. Cell-penetrating peptides (CPPs) that interact with membranes can improve the uptake of macromolecules across biological barriers. Here we explore methods for the peptide-mediated delivery of antisense oligonucleotides (ASOs) and chemotherapeutics. First, we address the issue that the optimal peptide sequence for the delivery of a macromolecular cargo is often context-dependent and specific to that cargo. With one class of ASO, we develop a paradigm that combines systematic screening of known CPPs in a functional assay for ASO delivery with machine learning methods. Using our computational model, we identify five novel sequences that increase ASO activity at least three-fold. Next, we demonstrate that combining CPPs of different classes generates chimeric peptides with synergistic effects on ASO delivery. These chimeras improve ASO activity twenty-fold, which is greater than any literature-reported sequence. Then, we examine peptide cyclization with perfluoroaryl-cysteine SNAr chemistry to improve the stability and delivery of peptide-ASO conjugates. We extend our SNAr chemistry to the synthesis of arginine-rich bicyclic peptides, which are more stable to proteolysis than single cycles. Both perfluoroaryl cyclic and bicyclic arginine-rich peptides improve ASO activity fourteen-fold. Consequently, we demonstrate that peptide cyclization with perfluoroaryl-cysteine SNAr chemistry enhances the ability of peptides to cross the BBB. We prepare macrocyclic analogues of both a CPP and a therapeutic peptide. We show that a subset of the macrocycles cross the BBB in both a cellular spheroid model of the BBB, as well as after intravenous injection in mice. Finally, we conjugate a platinum (IV) prodrug of the chemotherapeutic cisplatin to a brain-penetrating perfluoroaryl macrocycle and show that the amount of platinum in the mouse brain is fifteen-fold greater than cisplatin after five hours. In summary, we explore strategies to improve the peptide-mediated delivery of ASOs and small molecule chemotherapeutics across biological barriers. In the future, we envision extending these approaches to other macromolecular cargos of therapeutic interest."],"dc:description.degree":["Ph. D. in Biological Chemistry"],"dc:identifier.uri":["http://hdl.handle.net/1721.1/118259"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Chemistry."],"dc:title":["Peptide-mediated delivery of antisense oligonucleotides and chemotherapeutics across biological barriers"],"dc:type":["Thesis"]},"updated_at":"2026-07-22T22:22:08Z"}