New technique sheds light on the second secret of life: Allostery

This tool reveals the hidden ‘buttons’ that change the tasks performed by proteins. The finding could help accelerate the development of drugs to treat cancer and other diseases

A 3D image showing a human protein with another molecule (yellow) at the active site.
A 3D image showing a human protein with another molecule (yellow) at the active site.André Faure/CRG

Four years before winning the Nobel Prize for medicine, French biologist Jacques Monod arrived in the laboratory of a friend one night in 1961, and, with a tired face and after several minutes of silence, announced: “I believe that I have discovered the second secret of life.” His colleague, microbiologist Agnes Ullman, asked him if he needed a glass of whisky. By the third drink, Monod explained to him that he had observed an astonishing phenomenon: proteins, the genuine protagonists of life, had a type of hidden button that could change their function. Monod had even invented a word to describe that surprising transformation: allostery. More than half a century later, a team of scientists from Barcelona has discovered a method to identify those secret buttons. The authors argue that the system could “revolutionize” the discovery of drugs to treat cancer and other diseases.

Human cells contain a kind of recipe book – DNA, the first secret of life – to create proteins: keratin for the skin, collagen in the bones, myosin in muscles and hemoglobin in the blood. Simple molecules are easy to imagine, such as the alcohol in the whisky that Monod was drinking: it has two carbon atoms, six hydrogen and one oxygen: C₂H₅OH. Proteins, however, are chemical monsters that are often unfathomable. The formula for hemoglobin, for example, is C₂₉₅₂H₄₆₆₄N₈₁₂O₈₃₂S₈Fe₄. In the lungs, this giant combines with oxygen, causing a tri-dimensional change in structure that facilitates the union of more oxygen in other places. This is an example of allostery, a word with Greek roots that could be translated as “another structure.”

A team at the Center for Genomic Regulation (CRG) in Barcelona has now illuminated this second secret of life. Biologist Júlia Domingo compares the proteins with a microscopic car, which can be started with a physical key but also by “remote controls” hidden in the bodywork. “It’s hard to know where to look for them,” explains Domingo, who is now at the New York Genome Center. “Our method is to take the car and pull it to bits. We get the parts and analyze them one by one.”

The new technique creates thousands of versions of the same protein, with one or two mutations, and tests their properties in an automated way in living cells. The result is a map of supposed secret buttons, the so-called allosteric sites, which can serve to modify the function of the proteins using drugs. The CRG team, directed by the British biologist Ben Lehner, published their method on Wednesday in the magazine Nature.

Júlia Domingo provides an example. In 95% of the cases of pancreatic cancer, there are mutations in proteins called KRAS, which were considered to be immune to drugs for decades given that they lack obvious binding sites. The authors are already applying their method to these proteins and others of similar importance, to try to find their secret buttons.

“Normally, drugs are designed with a very random process and by serendipity,” she explains. “Companies begin with hundreds of thousands of candidates, without really knowing what they do. Our objective is to make a map of the allosteric landscapes, to know which properties the drugs should have. Instead of starting out blind, we will know where to direct the drugs.”

The Spanish biologist Júlia Domingo and the South African bioinformatics expert André Faure.
The Spanish biologist Júlia Domingo and the South African bioinformatics expert André Faure.Júlia Domingo

Proteins usually have an obvious starter key, the active site, which can be activated as if it were a switch. The big problem for medicine is that the active sites for different proteins are very similar, meaning that the medication aimed at these sites can alter many different proteins, causing major side effects. The allosteric pharmaceuticals, which are aimed at the secret buttons, are much more specific, explains Domingo, who signed the study along with South African bioinformatics data scientist André Faure and the German data scientist Jörn Schmiedel.

Many biotechnology companies have started to seek these secret doors to proteins over recent years. The American company Relay Therapeutics, for example, has raised nearly $1 billion (€917 million) to research potential allosteric pharmaceuticals for some tumors, such as breast cancer. “It’s the Holy Grail of pharmaceuticals,” states Júlia Domingo, who is 31 and from Barcelona.

The tool will facilitate the discovery of more efficient and safer pharmaceuticals
Chemist Nuria Campillo

One of the main scientific achievements of 2021 was when an artificial intelligence system, Google’s DeepMind, managed to predict with unprecedented precision the structure of nearly all of the proteins that make up a human being. The CRG scientists believe that their new method could serve to measure the effects of millions of mutations in thousands of proteins. An artificial intelligence system, they theorize, could use this vast quantity of data to take another major leap: predicting the function of a protein from its DNA recipe. In the opinion of the authors, this predictive capacity would “revolutionize” the development of medical treatments.

Victor Muñoz, a Spanish professor of bioengineering at the University of California, Merced, applauds the new method. “It’s a tool that could be useful to identify regions where the protein could be susceptible to being the target of a drug,” he says. But he is also cautious. The researcher also uses the example of a car. If the axle that connects the engine to the wheels is modified, the vehicle would stop working. That would be an allosteric change. “If you take a wheel off, the car would also not work, but that would be because it’s missing a part, not because you have touched something that is connected dynamically.”

In Muñoz’s opinion, the new method could reveal supposed allosteric sites that are no such thing. “They make massive mutations and they see that one has left the car broken, but you don’t know if it’s missing a wheel or an axle has been modified. You need more detailed information. You can use this method to identify a potentially interesting site, but afterwards you would have to do a lot more work to confirm it,” argues Muñoz, who is the director of the Center for Cellular and Bio-Molecular Machines (CCBM-CREST) at the University of California, Merced.

Chemist Nuria Campillo runs Aitenea Biotech, a company that is dedicated to research into and development of pharmaceuticals, and is supported by the Spanish National Research Council (CSIC). Campillo believes that the new method is “remarkable work, a very sleek way of identifying allosteric sites.” In her opinion, the tool will “facilitate the discovery of more efficient and safer pharmaceuticals.” The second secret of life is no longer so secret.

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