This finding could pave the way for the development of innovative and selective therapies aimed at halting tumor growth in the future.

The work was featured on the cover of the journal Science Signaling, from the Science group.

Kinases are enzymes that play a crucial role in cell communication and in the regulation of various functions in our body. Their main function is to transfer a phosphate group from a molecule called adenosine triphosphate (ATP) to other molecules, such as proteins. This functions as a switch, since passing the phosphate can “activate” or “inactivate” the modified protein, depending on each case. These signaling pathways are like “communication pathways” that allow cells to respond to external or internal stimuli.

The Chemical Biology of Regulatory Mechanisms group, led by Ricardo M. Biondi, has been studying for years the structure of PDK1, a protein kinase that plays a fundamental role in cell signaling and is closely linked to cell growth and survival. It is known that PDK1 has many substrates -or proteins- that it activates through this signaling pathway, and that in many types of cancer this pathway is potentiated, helping cancer cells to continue growing and surviving uncontrollably.

Members of the Chemical Biology of Regulatory Mechanisms group (from left to right): Ricardo Biondi, Alejandro Leroux, Mariana Sacerdoti, Macarena Acebedo and Lissy Gross.

As a result, AKT, one of the substrates that PDK1 activates and which is part of this signaling pathway, began to be studied. It was learned that if it is turned off, it can induce death in cancer cells, because they stop receiving the growth signal. The challenge then is how to turn off AKT: “It is very difficult to make a drug that turns off only one of the proteins, and if you turn off all of them, you can trigger toxic processes and the sometimes very harmful side effects”, said Mariana Sacerdoti, doctoral fellow and first author of the paper.

Discovering the structure

In this work they focused on studying PDK1 in its entirety: “Studying the structure of whole proteins (what they are like) is very difficult when they have two domains – something like two parts – as in this case, because you have to use different techniques and they are very complex”, explained Sacerdoti.

PDK1 has a kinase domain, which adds phosphate to substrates, and also a PH domain, whose function is to bind a lipid (PIP3) to the cell membrane. 

Using an interdisciplinary approach that included structural, bioinformatics and chemical biology techniques, the research group discovered what 3D form PDK1 takes when it does not phosphorylate AKT (i.e. does not activate it), but does activate other substrates. This mechanism is crucial not only because it indicates that it is possible to ‘turn off’ a single protein that is so relevant in cancer, but also because they found a molecule with which they could stabilize this conformation, achieving a selective inhibition of PDK1 substrate.

Cover of the journal Science Signaling. The figure shows two models of the structure of PDK1 alone (top) or with a compound (bottom) according to the results of a technique called SEC-SAXS.

“We are not inhibiting the kinase in its entirety, but we were able to inhibit only a small part: the activation of this substrate, while all its other functions that are so important for cell communication were preserved. This is the first time that this way of substrate-selective inhibition of PDK1 with respect to AKT has been described”, added Mariana.

So, through chemical biology techniques they were able to selectively block PDK1, to study a protein with two domains in solution in order to extract information from the structure and relate it to a functional consequence: it cannot activate its substrate when it is in the specific conformation they discovered.

In many types of cancer this signaling pathway is seen to be “more turned on” and PDK1 is one of the poles within this pathway. In summary, given that PDK1 activates several kinases that promote cell growth and survival, these results may provide ways to selectively manipulate PDK1 activity for future cancer treatments.

Lissy Gross and Alejandro Leroux from IBioBA; Sebastián Klinke from IIBBA; Mariela Bollini, Pedro Aramendía and Victoria Cappellari from CIBION, as well as foreign researchers from different international institutions such as the Frankfurt University Clinic, the European Molecular Biology Laboratory (EMBL), the University of Oxford, the University of Pittsburgh and the University of Singapore also participated in this study, which was highly interdisciplinary and collaborative.