Aptamer templated peptide ligation - on the way to synthtic ligases

• Applicant: Dr. Sebastian Pomplun
• Subject Area: Biological and Biomimetic Chemistry ; Biochemistry ; Organic Molecular Chemistry - Synthesis and Characterisation
• Term: from 2018 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 412851589

• Final Report Year: 2021

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

• De Novo Discovery of High Affinity Peptide Binders for the SARS-CoV-2 Spike Protein; ACS Central Science, 2021
  Pomplun, Sebastian; Jbara, Muhammad; Quartararo, Anthony J.; Zhang, Genwei; Brown, Joseph S.; Lee, Yen-Chun; Ye, Xiyun; Hanna, Stephanie & Pentelute, Bradley L.
  
• Discovery of nucleic acid binding molecules from combinatorial biohybrid nucleobase peptide libraries; JACS, 2020, 2020, 142, 46, 19642–19651
  Pomplun, Sebastian; Gates, Zachary P.; Zhang, Genwei; Quartararo, Anthony J. & Pentelute, Bradley L.
  
• Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release; Angew. Chem. Int. Ed. 2020, 59, 11566–11572
  Pomplun, Sebastian; Shugrue, Christopher R.; Schmitt, Adeline M.; Schissel, Carly K.; Farquhar, Charlotte E. & Pentelute, Bradley L.
  
• Engineering of bioactive transcription factors via flow synthesis and palladium crosscoupling; JACS, 2021, 143, 30, 11788
  Jbara, Muhammad; Pomplun, Sebastian; Schissel, Carly K.; Hawken, Susana Wilson; Boija, Ann; Klein, Isaac; Rodriguez, Jacob; Buchwald, Stephen L. & Pentelute, Bradley L.
  
• Parallel automated flow synthesis of covalent protein complexes that inhibit MYC-driven transcription, ACS Central Science, 2021, 7, 8, 1408–1418
  Pomplun, Sebastian; Jbara, Muhammad; Schissel, Carly K.; Wilson Hawken, Susana; Boija, Ann; Li, Charles; Klein, Isaac & Pentelute, Bradley L.
  
• Targeting the SARS-CoV-2-spike protein: from antibodies to miniproteins and peptides; RSC Med. Chem, 2020
  Pomplun, Sebastian