ALLOX aims to shape the future of medicine. The techbio company has just set up at the Barcelona Science Park and is emerging as one of the most promising startups in the Catalan biotechnology ecosystem. Its unique, systematic, and scalable technology promises to shed light on one of the most complex aspects of proteins, allosteric regulation, and open new opportunities to treat diseases, such as cancer, that have been difficult or impossible to address with conventional treatments.

Founded in 2023 by Júlia Domingo (CEO), André Faure (CDO), and Pablo Baeza (CSO) as a spin-off from the Centre for Genomic Regulation (CRG) of Barcelona with the support of Asabys Partners and CDTI Innovation, ALLOX has created an innovative platform that combines experimental genetics, artificial intelligence, and energy models. Its goal is to turn what was once considered unreachable in medicine: identifying elusive allosteric sites and turning them into new therapeutic targets for developing more effective treatments.

The three researchers met while working together in the laboratory of ICREA professor Ben Lehner, who is also a co-founder and Chief Scientific Advisor of the company. From their experience in studying genetic mutations, they began analysing how small changes in DNA affect the functioning of proteins, from their production to their shape and their ability to interact with other proteins. The pivotal turn in their research came when they realised that the technology not only allowed identifying the protein-protein interaction binding site, but also the more distant regulatory regions, called allosteric sites, that act as remote controls, and their modification can change the behaviour of the protein without altering its main structure.

Thanks to the use of deep mutational scanning, the researchers manage to map all possible mutations across an entire protein that affect its overall behaviour. The discovery revealed clusters of mutations close together in the protein structure that similarly affect is behaviour, suggesting the presence of “switches” on the protein surface that can modulate its function, and opening new possibilities for designing therapies that target protein activity in a more specific and effective way. The work, published in Nature journal, provides a general framework for identifying and better understanding allosteric mechanisms in proteins, revealing that allosteric regulation is more common and widespread than previously thought.

Allosteric modulators are one of the most promising frontiers in the development of innovative drugs. ALLOX’s long-term vision is to create the next generation of tools based on allosteric regulation, capable of predicting and designing new protein functions for the treatment of diseases such as cancer.

Mapping allostery: A versatile technology for treating multiple diseases

The ALLOX Bio platform is a combination of experimental and computational techniques, but the true uniqueness of its technology lies in its comprehensive nature. “Instead of making and testing individual mutations one by one, we can perform systematic mutagenesis of the entire protein,” explains André Faure. “It’s like turning on the lights in a dark room,” continues the researcher, allowing them to see the full picture of the protein. “Currently, we are applying our multidimensional mutagenesis technology to protein-protein interactions, a vast therapeutic area still mostly unaddressed, to understand how mutations affect these interactions and identify allosteric sites,” says Faure.

Allostery is a biological phenomenon that allows a protein to change its shape or function in response to external signals. Despite its importance, allostery remains a mystery because many of these allosteric sites are hidden and difficult to identify. They are “hidden switches” in proteins that play a crucial role in cellular regulation.

“The little we know about allosteric sites is that they can be excellent targets for drug discovery. Allosteric modulators turned out to be great therapies because they are much more specific to each protein, so they lead to fewer side effects and can overcome some of the clinical complications, such as toxicity,” explains Júlia Domingo.

Illuminating these hidden places in proteins allows the creation of allosteric maps that can serve as guides in the discovery of new targeted therapies for diseases that currently have no therapeutic options. “With our first maps, we realized that actually, allostery is widespread: there are many sites in proteins, outside the binding interface, or orthosteric site, that regulate that activity. So, it’s a very rich and potentially very valuable space to look for sites for new drug design,” explains André Faure.

“Our technology is target-independent, which allows us to apply it to a wide variety of proteins,” adds Júlia Domingo. “We started in the field of oncology because it has numerous validated disease-causing targets, but still the majority of these are exceptionally difficult to drug with conventional medicines. We are currently expanding our technology into other areas, such as immunology, where we focus on protein interactions in key biological pathways that could have a significant therapeutic impact,” concludes the company’s CEO.

The data generation and processing capabilities at ALLOX allows them to set short-term goals with great precision. As Pablo Baeza explains, “every day we generate more and more data from which we can learn, allowing us to fine-tune our predictions and understand how allostery works,” a field that remains uncertain. “At our company, we do experiments that result in huge amounts of data. All of this data gives us clues about the next steps to take, and so it is constantly guiding our business decisions,” clarifies Baeza.

For Júlia Domingo, this data generation could lay “the foundation for an innovative and more powerful artificial intelligence technology, capable of helping us predict and understand allosteric sites, guiding our experiments based on these predictions and opening the door to new targets that cannot be addressed with our current technology.”