Aptamer templated peptide ligation - on the way to synthtic ligases
Biochemistry
Organic Molecular Chemistry - Synthesis and Characterisation
Final Report Abstract
The de novo discovery of ligands for challenging and novel drug targets often requires the cumbersome screening of individual compounds from large libraries. I developed a fully chemistry based affinity selection – mass spectrometry (AS-MS) platform: within days synthetic polyamide compound libraries with > 100 million members can be produced, screened against targets of interest and originate hits with nanomolar affinity for their targets. I used AS-MS for the rapid discovery of synthetic high-affinity peptide binders for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The peptides display excellent selectivity for RBD over human serum proteins and can detect picomolar RBD concentrations in a biological matrix. I further expanded the AS-MS platform for the discovery of compounds targeting oncogenic pre-miRNA hairpins. In nature nucleic acids are often controlled by large supramolecular protein/oligonucleotide complexes as in the case of ribosomal protein synthesis. Rather than forming large complexes to coordinate the role of different biopolymers, I dovetailed protein amino acids and nucleobases into a single low molecular weight precision polyamide polymer. I established efficient chemical synthesis and de novo sequencing procedures and prepared combinatorial libraries with up to 100 million biohybrid molecules. This biohybrid material has a higher bulk affinity to oligonucleotides than peptides composed exclusively of canonical amino acids. Using affinity selection mass spectrometry, I discovered variants with a high-affinity for premicroRNA hairpins. Our platform points toward the development of high throughput discovery of sequence defined polymers with designer properties, such as oligonucleotide binding.
Publications
- Discovery of nucleic acid binding molecules from combinatorial biohybrid nucleobase peptide libraries; JACS, 2020, 2020, 142, 46, 19642–19651
Sebastian Pomplun, Zachary P. Gates, Genwei Zhang, Anthony J. Quartararo, and Bradley L. Pentelute
(See online at https://doi.org/10.1021/jacs.0c08964) - Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release; Angew. Chem. Int. Ed. 2020, 59, 11566–11572
Sebastian Pomplun, Christopher Shugrue, Adeline Schmitt, Carly Schissel, Charlotte Farquhar, Bradley L. Pentelute
(See online at https://doi.org/10.1002/anie.202003478) - Targeting the SARS-CoV-2-spike protein: from antibodies to miniproteins and peptides; RSC Med. Chem, 2020
Sebastian Pomplun
(See online at https://doi.org/10.1039/D0MD00385A) - De Novo Discovery of High Affinity Peptide Binders for the SARS-CoV-2 Spike Protein; ACS Central Science, 2021
Sebastian Pomplun, Muhammad Jbara, Anthony J. Quartararo, Genwei Zhang, Joseph Brown, Yen-Chun Lee, Xiyun Ye, Stephanie Hanna and Bradley L. Pentelute
(See online at https://doi.org/10.1021/acscentsci.0c01309) - Engineering of bioactive transcription factors via flow synthesis and palladium crosscoupling; JACS, 2021, 143, 30, 11788
Muhammad Jbara, Sebastian Pomplun, Carly Schissel, Susanne Wilson Hawken, Jacob Rodrigues, Ann Boija, Isaac Klein, Richard Young, Stephen L. Buchwald and Bradley L. Pentelute
(See online at https://doi.org/10.1021/jacs.1c05666) - Parallel automated flow synthesis of covalent protein complexes that inhibit MYC-driven transcription, ACS Central Science, 2021, 7, 8, 1408–1418
Sebastian Pomplun, Muhammad Jbara, Carly Schissel, Ann Boija, Susanne Wilson Hawken, Isaac Klein, and Bradley L. Pentelute
(See online at https://doi.org/10.1021/acscentsci.1c00663)
