Supramolecular Entrapment of PTMs and Modulation of Epigenetic Control

• Applicants: Professor Dr. Peter Bayer; Professor Dr. Thomas Schrader
• Subject Area: Biological and Biomimetic Chemistry ; Organic Molecular Chemistry - Synthesis and Characterisation
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 417579646

• Final Report Year: 2023

Final Report Abstract

This research endeavour is all about recognition and imitation of posttranslational modifications by Supramolecular Chemistry. In two separate projects we demonstrate how designed molecular clips and tweezers can be used for the entrapment of post-translationally modified amino acids and for the modulation of histones to affect and influence epigenetic DNA patterns. In Project 1, tailored modification of ADMA-selective molecular clips significantly increased their affinity, but unfortunately did not maintain their preference for dimethylated arginine species. On the other hand, Glycoluril derivative Motor 1 (M1) matches our requirement for a selective entrapment of this dangerous methylated species in the presence of free arginine. In a new in-vitro assay established in our lab, we were able to provide a proof-of-principle for our postulated competitive MA entrapment by a supramolecular host: eNOS inhibition by methylated arginines could be restored by adding the supramolecular host Motor 1 (M1). With our new in-vivo assay, we hope to be able to demonstrate the same effect also in cell culture. In Project 2, a large number of novel tweezer derivatives was synthesized, in order to target the DNA binding site on histone peptide H4. The high density of basic amino acids inside the H4-P1 fragment was addressed by an acidic peptide stretch attached to the parent tweezer CLR01 by a click protocol. Its charge complementarity should greatly enhance its affinity towards this lysine and arginine cluster. In addition, various artificial binding motifs for lysines, arginines and histidines were introduced as central linkers into a dimeric tweezer construct by a newly established iterative click reaction. These dimeric tweezers turned out to be highly selective for H4-P1, the DNA binding site, and displayed exquisite affinities in phosphate buffer reaching the one digit nanomolar regime. With the best binders, a competitive displacement of DNA bound to the histone peptide was demonstrated. In addition, stoichiometric amounts of dimeric tweezers complexed the DNA binding site of the histone peptide and inhibited the enzymatic activity of histone-acetyltransferase HAT in a dose-dependent manner. Thus, powerful new histone binders were developed which could act as supramolecular PTM on a histone H4 peptide.

Publications

• Supramolecular Mechanism of Viral Envelope Disruption by Molecular Tweezers. Journal of the American Chemical Society, 142(40), 17024-17038.
  Weil, Tatjana; Groß, Rüdiger; Röcker, Annika; Bravo-Rodriguez, Kenny; Heid, Christian; Sowislok, Andrea; Le, My-Hue; Erwin, Nelli; Dwivedi, Mridula; Bart, Stephen M.; Bates, Paul; Wettstein, Lukas; Müller, Janis A.; Harms, Mirja; Sparrer, Konstantin; Ruiz-Blanco, Yasser B.; Stürzel, Christina M.; von Einem, Jens; Lippold, Sina ... & Münch, Jan
  
• Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes**. ChemBioChem, 23(2).
  Warmerdam, Zoey; Kamba, Bianca E.; Le, My‐Hue; Schrader, Thomas; Isaacs, Lyle; Bayer, Peter & Hof, Fraser
  
• Calix[4]arene sulfonate hosts selectively modified on the upper rim: a study of nicotine binding strength and geometry. Supramolecular Chemistry, 33(4), 88-96.
  Warmerdam, Zoey; Kamba, Bianca E.; Shaurya, Alok; Sun, XuXin; Maguire, Mary K. & Hof, Fraser
  
• Advanced Molecular Tweezers with Lipid Anchors against SARS-CoV-2 and Other Respiratory Viruses. JACS Au, 2(9), 2187-2202.
  Weil, Tatjana; Kirupakaran, Abbna; Le, My-Hue; Rebmann, Philipp; Mieres-Perez, Joel; Issmail, Leila; Conzelmann, Carina; Müller, Janis A.; Rauch, Lena; Gilg, Andrea; Wettstein, Lukas; Groß, Rüdiger; Read, Clarissa; Bergner, Tim; Pålsson, Sandra Axberg; Uhlig, Nadja; Eberlein, Valentina; Wöll, Heike; Klärner, Frank-Gerrit ... & Münch, Jan
  
• Molecular tweezers – a new class of potent broad-spectrum antivirals against enveloped viruses. Chemical Communications, 58(18), 2954-2966.
  Le, My-Hue; Taghuo, K. Estelle S. & Schrader, Thomas