Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization
Chapter 1: Bicyclic peptides have been developed to mimic good binders that structurally resemble antibody mimetics. The identity of the linker plays a critical role in enforcing the structure of the cyclic entity. Palladium-mediated arylation has enabled cysteine-specific modifications with a numbe...
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| Format: | Thesis |
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Massachusetts Institute of Technology
2022
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| Online Access: | https://hdl.handle.net/1721.1/140354 |
| _version_ | 1811096282107740160 |
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| author | Mallek, Aaron J. |
| author2 | Buchwald, Stephen L. |
| author_facet | Buchwald, Stephen L. Mallek, Aaron J. |
| author_sort | Mallek, Aaron J. |
| collection | MIT |
| description | Chapter 1: Bicyclic peptides have been developed to mimic good binders that structurally resemble antibody mimetics. The identity of the linker plays a critical role in enforcing the structure of the cyclic entity. Palladium-mediated arylation has enabled cysteine-specific modifications with a number of previously inaccessible aryl groups. Mono-Pd oxidative addition complexes (OACs) derived from 1,3,5-triiodobenzene enable iterative C–S arylation around the benzene scaffold through regeneration of the active palladium site. This reagent is successfully used to generate a highly rigid, benzene linked bicyclic variant of a human plasma kallikrein inhibitor. A nearly 5000-fold loss in inhibitory activity demonstrates the potential difference in bioactivity accessed by this chemical change. In addition to potential application as a bicyclic linker, peptide cross-linking is achieved in high conversion using peptides containing a single cysteine. Furthermore, linear and cyclic peptide OACs are accessible through non-exhaustive C–S arylation, leaving the active Pd(II) site intact for future functionalization to small molecules or other biomolecules.
Chapter 2: Macrocyclic peptides hold immense potential for targeting “undruggable” protein-protein interactions as their expanded surface areas enable increasingly complex surface interactions. Unlike biologics however, peptides are highly synthetically accessible and may be readily modified to enhance binding interactions, proteolytic stability, and intracellular access. High throughput techniques such as mRNA and phage display have been instrumental for discovering new peptidic protein ligands, however these techniques are limited with respect to incorporation of non-canonical amino acids. Synthetic libraries used in solution phase affinity selection-mass spectrometry (AS-MS) enable the use of nearly limitless non-canonical residues, however this approach is not compatible with macrocyclic peptides. Herein, we target cysteine-linked macrocycles for mild oxidation to the sulfoxide and subsequent base-promoted elimination to linearize the macrocycle and form a dehydroalanine adduct for further modification. This approach is used to successfully linearize stapled peptides and aryl/alkyl-linked bicyclic peptides. Furthermore, the protocol maintained sequencing integrity even with as little as 50 pg of peptide demonstrating viability for use with synthetic libraries in affinity selection-mass spectrometry.
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Chapter 3: The selective N-arylation of p-aminophenylalanine in polypeptides with pre-formed palladium oxidative addition complexes is described. The depressed pKa of the aniline NH2 group enables chemoselective C−N bond formation on peptides containing multiple other aliphatic amino groups at lysines or the N-terminus via Curtin-Hammett control under mild conditions. Using palladium complexes derived from electron-poor aryl halides, p-aminophenylalanine is fully arylated in aqueous buffer in as little as one hour at micromolar concentrations. A complementary protocol using the non-nucleophilic, organic base 1,5-diazabicyclo(4.3.0)non-5-ene (DBN), expands the substrate scope to tolerate electron-rich functional groups provides up to 97 % conversion. These procedures enable the chemoselective conjugation of functionally diverse small molecule pharmaceuticals to p-aminophenylalanine containing derivatives of cell-penetrating peptides. |
| first_indexed | 2024-09-23T16:41:25Z |
| format | Thesis |
| id | mit-1721.1/140354 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T16:41:25Z |
| publishDate | 2022 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1403542022-02-16T03:01:34Z Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization Mallek, Aaron J. Buchwald, Stephen L. Pentelute, Bradley L. Massachusetts Institute of Technology. Department of Chemistry Chapter 1: Bicyclic peptides have been developed to mimic good binders that structurally resemble antibody mimetics. The identity of the linker plays a critical role in enforcing the structure of the cyclic entity. Palladium-mediated arylation has enabled cysteine-specific modifications with a number of previously inaccessible aryl groups. Mono-Pd oxidative addition complexes (OACs) derived from 1,3,5-triiodobenzene enable iterative C–S arylation around the benzene scaffold through regeneration of the active palladium site. This reagent is successfully used to generate a highly rigid, benzene linked bicyclic variant of a human plasma kallikrein inhibitor. A nearly 5000-fold loss in inhibitory activity demonstrates the potential difference in bioactivity accessed by this chemical change. In addition to potential application as a bicyclic linker, peptide cross-linking is achieved in high conversion using peptides containing a single cysteine. Furthermore, linear and cyclic peptide OACs are accessible through non-exhaustive C–S arylation, leaving the active Pd(II) site intact for future functionalization to small molecules or other biomolecules. Chapter 2: Macrocyclic peptides hold immense potential for targeting “undruggable” protein-protein interactions as their expanded surface areas enable increasingly complex surface interactions. Unlike biologics however, peptides are highly synthetically accessible and may be readily modified to enhance binding interactions, proteolytic stability, and intracellular access. High throughput techniques such as mRNA and phage display have been instrumental for discovering new peptidic protein ligands, however these techniques are limited with respect to incorporation of non-canonical amino acids. Synthetic libraries used in solution phase affinity selection-mass spectrometry (AS-MS) enable the use of nearly limitless non-canonical residues, however this approach is not compatible with macrocyclic peptides. Herein, we target cysteine-linked macrocycles for mild oxidation to the sulfoxide and subsequent base-promoted elimination to linearize the macrocycle and form a dehydroalanine adduct for further modification. This approach is used to successfully linearize stapled peptides and aryl/alkyl-linked bicyclic peptides. Furthermore, the protocol maintained sequencing integrity even with as little as 50 pg of peptide demonstrating viability for use with synthetic libraries in affinity selection-mass spectrometry. 6 Chapter 3: The selective N-arylation of p-aminophenylalanine in polypeptides with pre-formed palladium oxidative addition complexes is described. The depressed pKa of the aniline NH2 group enables chemoselective C−N bond formation on peptides containing multiple other aliphatic amino groups at lysines or the N-terminus via Curtin-Hammett control under mild conditions. Using palladium complexes derived from electron-poor aryl halides, p-aminophenylalanine is fully arylated in aqueous buffer in as little as one hour at micromolar concentrations. A complementary protocol using the non-nucleophilic, organic base 1,5-diazabicyclo(4.3.0)non-5-ene (DBN), expands the substrate scope to tolerate electron-rich functional groups provides up to 97 % conversion. These procedures enable the chemoselective conjugation of functionally diverse small molecule pharmaceuticals to p-aminophenylalanine containing derivatives of cell-penetrating peptides. Ph.D. 2022-02-15T17:01:35Z 2022-02-15T17:01:35Z 2021-06 2021-06-16T17:28:17.118Z Thesis https://hdl.handle.net/1721.1/140354 0000-0001-8642-8152 In Copyright - Educational Use Permitted Copyright MIT http://rightsstatements.org/page/InC-EDU/1.0/ application/pdf application/pdf Massachusetts Institute of Technology |
| spellingShingle | Mallek, Aaron J. Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title | Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title_full | Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title_fullStr | Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title_full_unstemmed | Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title_short | Organometallic Palladium Reagents for Polypeptide Bioconjugation and Macrocyclization |
| title_sort | organometallic palladium reagents for polypeptide bioconjugation and macrocyclization |
| url | https://hdl.handle.net/1721.1/140354 |
| work_keys_str_mv | AT mallekaaronj organometallicpalladiumreagentsforpolypeptidebioconjugationandmacrocyclization |