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Stringing Science Together: Bead-azzling Macrocyclization for Biochemistry Bling

8 December 2023
Imagine making a necklace. You start with various colors and shapes of beads, and you decide which specific beads you want to connect to form a circle. The selected beads will then be secured together to form a loop. Depending on the desired look, you can connect different types of beads to create distinct and unique necklaces. Finally, your choice on the type of clasp determines how difficult it is to close the necklace, a magnetic clasp can be easier to close than a lobster claw for example.

This is the essence of macrocyclization, wherein small molecules are chemically linked together to form a large ring-like structure. Macrocyclization is an important addition to the mRNA display technique for in vitro peptide evolution to discover molecules that can bind to desired biological targets. A research team from AIMMS VU, led by Seino Jongkees, has developed a new approach to peptide macrocyclization using cyanobenzothiazole (CBTz). They published the properties and the synthesis of this macrocyclization in Chemistry: A European Journal.

mRNA display is a method used to discover molecules that can bind to specific biological targets. First, researchers make a huge number of very small proteins called peptides that are each connected to their building instructions (mRNA) via a molecule called puromycin (1). Then, they see which of these peptides can stick best to our target (2). The ones that stick well are copied and the instructions turned back into a DNA code (3). This code holds the recipe for a peptide with high affinity for the molecule of interest.

Using macrocyclic peptides in mRNA display is a powerful technique to discover high affinity ligands for a protein target. Compared to non-macrocyclized peptides, macrocyclization allows the peptide to mimic natural products (4 and 5) and therefore increases cell permeability, structure stability and rigidity, alongside decreasing degradation due to the structural constraints of macrocycles. However, only a limited number of cyclization chemistries are known to be compatible with mRNA display. Existing macrocyclization methods in mRNA display have issues such as high flexibility and no regioselectivity.

The research team, led by Seino Jongkees, at Vrije Universiteit Amsterdam has succeeded in creating a new macrocyclization technique using CBTz. This technique not only has navigated past most drawbacks of current methods (6), but also allows more chemical modifications of the peptide and gives different functionality than the most commonly used macrocyclization method which is by using a thioether. The research team has done computational studies to determine and visualise the molecular differences of CBTz compared to thioethers. They conclude that the inherent differences in their structures influence the folding of the resulting peptide through enhanced rigidity and increased aromatic interactions. Consequently, this induces a change in the activity of the resulting peptide. The next step in unravelling its potential is to use this methodology to discover new peptides against disease-relevant targets and analyse their effects in vitro and in vivo.

In essence, macrocyclization involves taking smaller molecules and chemically linking them in a specific way to create a larger ring-shaped molecule. This can have various uses including new materials creation, designing drugs, or understanding biological processes. Just like with jewelry making, you’re essentially building a big loop or ring from smaller pieces, but in chemistry, it's done through chemical reactions. Certain ways of building the loop are more efficient and easier to bind to our biological targets. Thus, with this new and improved method of constructing the loop (macrocyclization), the toolbox that researchers have at their disposal has become more complete. They have concluded that by utilizing this cyclisation reaction, we can discover new and different hits, resulting in potential novel therapeutic compounds for desired targets.



Macrocyclization using cbtz as thioether