How reprogramming cells can degrade harmful proteins and combat diseases
Ubiquitin is a small protein present in the cells of almost all organisms. It is – nomen est omen – literally ubiquitous. In 2004, the Nobel Prize in Chemistry was awarded for the discovery of ubiquitin’s role in the cell’s disposal system for defective or superfluous proteins. Together with partners in the Cluster4Future PROXIDRUGS, Ivan Đikić is using these findings to reprogram cells that are at the heart of neurodegenerative diseases, infections or cancer. Their common goal is to find new drugs to treat these diseases.
Many diseases are triggered by mutations that result in a protein working insufficiently or even being completely absent. However, there are also diseases that are caused by too many proteins: A protein that is too abundant or overactive can also make us ill. Especially in cancer, uncontrolled cell growth is mostly mediated by overactive signaling pathways or regulators of cell division.
One way of suppressing the growth of cancer cells is to inhibit the relevant cellular components. This is often done with specific inhibitors – small compounds whose three-dimensional structure enables them to bind selectively to the active center of an enzyme or the binding site of a regulator, thus preventing its pathogenic activity.
However, medicine often reaches its limits with this approach. Often no specific inhibitors are known, which is why researchers are now searching systematically for such substances (see also “Toolbox for new drugs”, page 57). In addition, many proteins do not have suitable binding sites for inhibitors. More than 75% of all known proteins are therefore deemed to be “undruggable”, i.e. they cannot be targeted by drugs.
A new therapeutic approach entirely abandons classic inhibitors. Instead, it relies on reprograming the cellular waste disposal system and having the cell itself eliminate harmful proteins. This approach works not only for proteins that are overactive or produced in excessive numbers, but also for those that cause damage due to an incorrect structure or function. Examples are “plaques”, protein aggregates that lead to cell death in neurodegenerative diseases such as Alzheimer’s or Parkinson’s disease.
Recycling inside the cell
But how can a protein be degraded as selectively as possible inside a cell? Ivan Đikić wants to utilize the cell’s own “ubiquitin” recycling system for this purpose. The Croatian physician and biochemist has long been studying the small protein ubiquitin, which is found in all higher organisms and forms the core component of a cellular waste system. This mechanism, known as the ubiquitin-proteasome system (UPS), breaks down proteins into their components – the amino acids – and directs them towards cellular recycling, such that new proteins can be produced.
The UPS is just one of the cell’s recycling systems, yet it is responsible for disposing of a remarkable number of proteins involved in cancer development. Đikić first encountered ubiquitin while studying a group of proteins that promote cancer. “In my doctoral thesis, I examined how overactive growth factor receptors contribute to cancer development. These receptors are controlled by ubiquitin, among other things.” Indeed, defects in the cellular waste system are found in some tumor types and also in many neurodegenerative diseases.
Tagged as “trash”
Small, but versatile: Ubiquitin is responsible for a lot more than just protein degradation, continues Đikić: “It plays an important role in the regulation of many important processes in the cell. That’s why studying it never gets boring, and new, surprising discoveries are constantly made.” For instance, knowledge about how bacteria and viruses that lack ubiquitin manipulate the host’s UPS to weaken immune responses is still relatively new.
Ubiquitin can be thought of as a kind of “tag”: Attaching it to a protein tells the cellular machinery what to do with it. The link is always made between ubiquitin and amino acids in the target proteins that provide a suitable chemical group.
There are two possibilities here: Ubiquitin can either be attached to a protein as a single molecule or in the form of differently branched ubiquitin chains. The researchers describe this as a code that triggers different effects in the cell, depending on the type of linkage and branching of the attached ubiquitin chains. For them to serve as a degradation signal, several ubiquitin units must be linked in a very specific way. Proteins marked in this way are recognized by a central component of the UPS, the proteasome. The proteasome functions like a shredder, formed like a cylinder with several enzymes lining its inner wall. The UPS is an important quality assurance system for the cell. It has long been known that failure of this system leads to cell damage and the development of diseases, explains Đikić: “However, intensive research into the UPS has also helped us to recognize that ubiquitin can be used as a powerful tool to systematically eliminate harmful proteins.”
4 If the cell is not sufficiently supplied with nutrients, it starts to degrade its own components. Shown here, for example, is the endoplasmic reticulum, a system of tubular structures. The parts to be degraded (pale green) are broken down in small vesicles (lysosomes, magenta).
5 The cell constantly renews its power plants, the mitochondria (green). They are broken down in the lysosomes located near the cell nucleus (blue). Red: the cytoskeleton of actin filaments. Photos 2+3 Yangxue Fu, AG Đikić, 4 Grumati et al. eLife 2017 https://doi.org/10.7554/eLife.25555, 5 Dr. Alexandra Hertel
Forced proximity
Proximity-inducing drugs (proxidrugs) facilitate the targeted degradation of specific proteins by the UPS. The idea behind this is actually quite simple, as Đikić explains: “You induce the transfer of ubiquitin chains to the target protein and thus mark it for the proteasome shredder.” To initiate this, a compound is used to bring the target protein into direct proximity of the ubiquitin-transferring enzyme, the E3 ligase. Different types of structures for proxidrugs are available. To date, PROTACs (proteolysis targeting chimeras) and molecular glues are the most advanced.
“The best-known molecular glue is thalidomide, the drug that was heavily discredited due to its severe side effects that became apparent during its wide use as a sedative and antiemetic,” explains Đikić. “Today we know that thalidomide is very effective against multiple myeloma.” Science now has a better understanding of how thalidomide works – the small molecule binds to an E3 ubiquitin ligase and can, for example, reprogram the ligase’s function and trigger the degradation of other proteins. In multiple myeloma, signaling proteins (transcription factors) are responsible for the uncontrolled growth of cancer cells. Thalidomide literally glues the E3 ubiquitin ligase and the signaling proteins together.
While the molecular glues known to date were discovered more or less by serendipity, PROTACs are being developed rationally. PROTACs are molecules with two subunits that can be imagined as Lego bricks connected to each other via a short string – the linker. One of the “bricks” has a binding site for the E3 ubiquitin ligase, the other for the target protein. In principle, any cellular protein can be brought into contact with any ligase in this way. However, PROTACs are significantly larger than molecular glues, which makes it more difficult to get them into the cell. This is why it took around 15 years for the first PROTAC-based drug to become available – an anti-breast cancer that has been tested on patients in phase III trials since 2023.
Basis for novel therapies
Advancing the development of such compounds is the goal of the PROXIDRUGS cluster coordinated by Ivan Đikić (see box). “The idea is to bring together experts from the Rhine-Main region and beyond to functionalize the ubiquitin system for the development of new drugs,” says Đikić. “We are very proud that our project was one of only seven selected out of 137 projects for the first round of funding in the extremely competitive Clusters4Future initiative. Together with our academic and commercial partners, we now want to tackle the challenges on the way towards targeted proximity-inducing drugs against cancer, neurodegenerative and infectious diseases.” This also includes finding ways of delivering proxidrugs to their respective target sites, for example the brain or other organs.
Among other things, the researchers are endeavoring to make better use of the natural diversity of E3 ubiquitin ligases, as Đikić explains: “Of the more than 600 variants that occur in human cells, we currently use mainly two.” At first glance, this is not an issue, as the mode of action of PROTACs reprograms the natural specificity of each ligase for certain proteins. “But the ligases we use are also active in healthy cells,” notes Đikić, “meaning that a PROTAC can trigger undesirable effects.” It would therefore be better to use a ligase that is significantly more active in the target tissue – for example in certain cancer cells – than in healthy cells.
The instruments and technologies used in the search for suitable PROTAC candidates have been bundled within the “Frankfurt Competence Center for Emerging Therapeutics (FCET)”. FCET was founded as a competence center within the framework of the “Goethe Center for (High) Technology (Go4Tec)”. According to Đikić, FCET provides everything needed from the design of active compounds to their validation in animal models. “Our culture of interdisciplinarity and teamwork is the key to our success,” emphasizes the biochemist. “It is this exchange across scientific disciplines that makes our work truly efficient.” Đikić is already dreaming of expanding the PROXIDRUGS cluster even further in the second funding phase: “We would like to integrate our technology with the mRNA technology on which the COVID-19 vaccines from Mainz-based BioNTech are based by bringing together PROXIDRUGS researchers from Frankfurt and mRNA researchers from Mainz.”
Proxidrugs / Degradation of target structures as a novel mode of action for drugs Researchers in the Cluster4Future PROXIDRUGS are developing novel drugs – so-called proximity-inducing drugs (proxidrugs) – that specifically degrade disease-relevant proteins in the body. In a cross-institutional network, PROXIDRUGS aims to establish infrastructure and workflows for the design, synthesis, characterization and optimization of proxidrugs and, ultimately, their transfer to clinical trials. The cluster is coordinated by Ivan Đikić at Goethe University Frankfurt. Other academic partners participating are TU Darmstadt, Heidelberg University, the Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and the Max Planck Institute of Biophysics. Several pharmaceutical companies are also involved. For the first implementation phase from 2021 to 2024, PROXIDRUGS was funded with €14 million within the Clusters4Future initiative of the Federal Ministry of Education and Research (BMBF). In 2024, PROXIDRUGS was able to raise up to €15 million for the second three-year implementation phase. The cluster, which was originally initiated by three academic partner institutions, has now grown to over 20 partners from science, biotechnology and the pharmaceutical industry.
About / Ivan Đikić, born in 1966, is Director of the Institute of Biochemistry II at Goethe University Frankfurt. He completed his medical degree in Zagreb (Croatia) and then earned his doctoral degree in molecular biology at New York University. After working as a group leader at the Ludwig Institute for Cancer Research in Uppsala (Sweden), Đikić was appointed as Professor of Biochemistry at the Faculty of Medicine, Goethe University Frankfurt, in 2002. He was the founding director of the Buchmann Institute for Molecular Life Sciences (BMLS), where he continues to head a research group. He is also a fellow at the Max Planck Institute of Biophysics. Besides leading the BMBF-funded Clusters4Future PROXIDRUGS, he is also a spokesperson of the German Research Foundation (DFG)-funded Collaborative Research Center 1177 on selective autophagy and ENABLE, a cluster project of the State of Hesse. In 2013, he received the Gottfried Wilhelm Leibniz Prize, the highest scientific honor in Germany; in 2023, he was awarded the Louis-Jeantet Prize for Medicine for his outstanding scientific achievements in the field of ubiquitination.
dikic@biochem2.uni-frankfurt.de
The author / Larissa Tetsch studied biology and earned her doctoral degree in microbiology. She then worked in basic research and later in medical training. She has been working as a freelance science and medical journalist since 2015 and is also the managing editor of the science magazine “Biologie in unserer Zeit”.
