Many of the key proteins for modern medicine and science are poorly soluble. These include numerous signalling proteins and protein hormones, as well as all of the receptors anchored in the cell membranes, which are targeted by around 60 percent of the active ingredients currently used in medicines. If the concentration of these proteins exceeds a certain threshold, they clump together and lose their function.
This clumping makes it impossible to produce these molecules synthetically in the lab. As protein production with specialised synthesis robots always requires multiple fragments to be coupled into a complete protein, just one poorly soluble protein segment is usually enough to block production. This is because the existing methods used by chemists to join up protein fragments only work if these fragments are present in solution at relatively high concentrations.
Researchers led by Jeffrey Bode, a professor at the Laboratory of Organic Chemistry of ETH Zurich, have now found a way to couple even poorly soluble protein segments into functioning proteins. To do so, they made use of the special properties of a chemical compound containing the element boron.
Slow carbon chemistry imposes concentration limits
The big difference between the ETH method and the conventional approaches lies in the speed of the coupling reaction. Whereas biochemistry takes place very quickly in the cells of organisms thanks to enzymes, reactions of this kind generally have to be performed at unnaturally high concentrations in the laboratory. This is because the slower a reaction occurs, the higher the concentration of the reacting substances must be for it to work as planned.
The new coupling method developed by Bode's group is around 1,000 times faster and therefore also works at 1,000 times lower concentrations.
Boron paves the way for new chemical possibilities
The ETH chemists accelerated the reaction by introducing boron atoms into the carbon-based molecules. These atoms do not appear in natural molecules.
In terms of many of its properties, the metalloid boron acts rather differently. When it bonds with metals, it produces extremely hard and heat-resistant metal alloys. On the other hand, it can bond with the nonmetals carbon, oxygen or nitrogen in the laboratory to produce molecules that often exhibit unusual reaction properties. In 2010, the Japanese researcher Akira Suzuki and the American researcher Richard Heck were awarded the Nobel Prize in Chemistry for the development of boron-based coupling reactions for the laboratory synthesis of natural substances.
Bode explains: "With purely carbon based systems, we hit a fundamental limit of reaction rates. By extending into previously unexplored boron-based reagents, we enter a realm in which even challenging reactions coupling large biological molecules together can take place extremely quickly."
A rocky road to protection against strong acids
In 2012, Bode's research group showed for the first time that a carbon compound in which boron was combined with fluorine to create a new chemical group could join protein fragments extremely quickly and reliably. However, this compound was not stable in the presence of strong acids and therefore could not be used in automated synthesis.
For the sensitive boron compound to withstand the harsh conditions used in standard laboratory robots, it would need a protective chemical packaging – but this was easier said than done. The researchers tested various strategies for four years, largely without success.
The breakthrough eventually came by chance, when a doctoral student tested an approach that the team had actually believed didn't work. The resulting protective compound "grips" the boron group from three sides, so that it cannot be broken down by the acids during protein production.
Bode says: "This kind of fundamental research, where we can venture into uncharted scientific territory with no guarantee of success, is only possible thanks to unrestricted funds from the Swiss National Science Foundation and ETH."
Unnatural amino acids and cancer therapies
The ETH method means it is now possible to produce new peptide and protein medications or medically important membrane proteins that are susceptible to clumping using standard laboratory techniques.
In addition, unnatural amino acids with special properties can also be introduced at any desired position on poorly soluble proteins. For example, chemists can incorporate these building blocks into a protein in a targeted manner if they want to link it to an active substance at a specific position. Among other applications, antibody–drug conjugates created in this way are used in cancer therapies that do not harm healthy tissue.
It is not yet clear how the method will be used in clinical practice. In 2020, Bode cofounded the ETH spin-off Bright Peak Therapeutics, which uses the technologies developed in his research group to develop immunotherapies for fighting cancer. An initial therapeutic agent is already undergoing clinical trials, and the new boron-based method could help to further expand the spin-off's product pipeline.
