{"id":83532,"date":"2025-05-12T10:00:00","date_gmt":"2025-05-12T08:00:00","guid":{"rendered":"https:\/\/aktuelles.uni-frankfurt.de\/?p=83532"},"modified":"2025-05-12T14:01:22","modified_gmt":"2025-05-12T12:01:22","slug":"targeted-removal-of-disease-triggers","status":"publish","type":"post","link":"https:\/\/aktuelles.uni-frankfurt.de\/en\/english\/targeted-removal-of-disease-triggers\/","title":{"rendered":"Targeted removal of disease triggers"},"content":{"rendered":"

How reprogramming cells can degrade harmful proteins and combat diseases<\/h2>\n\n\n\n

Ubiquitin is a small protein present in the cells of almost all organisms. It is \u2013 nomen est omen<\/em> \u2013 literally ubiquitous. In 2004, the Nobel Prize in Chemistry was awarded for the discovery of ubiquitin\u2019s role in the cell\u2019s disposal system for defective or superfluous proteins. Together with partners in the Cluster4Future PROXIDRUGS, Ivan \u0110iki\u0107 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.<\/strong><\/p>\n\n\n\n

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Dr. Ah Jung Heo, a postdoctoral researcher in the \u0110iki\u0107 group, is investigating how disease-relevant proteins could be selectively degraded. Photo: Peter Kiefer<\/figcaption><\/figure>\n\n\n\n
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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.<\/p>\n\n\n\n

One way of suppressing the growth of cancer cells is to inhibit the relevant cellular components. This is often done with specific inhibitors \u2013 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.<\/p>\n\n\n\n

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 \u201cToolbox for new drugs\u201d, 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 \u201cundruggable\u201d, i.e. they cannot be targeted by drugs.<\/p>\n\n\n\n

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 \u201cplaques\u201d, protein aggregates that lead to cell death in neurodegenerative diseases such as Alzheimer\u2019s or Parkinson\u2019s disease.<\/p>\n\n\n\n

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Recycling inside the cell<\/h3>\n\n\n\n
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Molecular glues or engineered chimeric molecules (PROTACS) direct harmful proteins to the cellular recycling system. They bring the target protein into close proximity to the enzyme E3 ligase, which in turn attaches a chain of ubiquitin units to the target protein. Labelled for disposal, the target protein is degraded in the proteasome. Diagram: AG \u0110iki\u0107; created with BioRender; Designua, Honourr \u2013 shutterstock.com. Layout by artefont<\/figcaption><\/figure>\n\n\n\n

But how can a protein be degraded as selectively as possible inside a cell? Ivan \u0110iki\u0107 wants to utilize the cell\u2019s own \u201cubiquitin\u201d 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 \u2013 the amino acids \u2013 and directs them towards cellular recycling, such that new proteins can be produced.<\/p>\n\n\n\n

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. \u0110iki\u0107 first encountered ubiquitin while studying a group of proteins that promote cancer. \u201cIn my doctoral thesis, I examined how overactive growth factor receptors contribute to cancer development. These receptors are controlled by ubiquitin, among other things.\u201d Indeed, defects in the cellular waste system are found in some tumor types and also in many neurodegenerative diseases.<\/p>\n\n\n\n

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Tagged as \u201ctrash\u201d<\/h3>\n\n\n\n

Small, but versatile: Ubiquitin is responsible for a lot more than just protein degradation, continues \u0110iki\u0107: \u201cIt plays an important role in the regulation of many important processes in the cell. That\u2019s why studying it never gets boring, and new, surprising discoveries are constantly made.\u201d For instance, knowledge about how bacteria and viruses that lack ubiquitin manipulate the host\u2019s UPS to weaken immune responses is still relatively new.<\/p>\n\n\n\n

Ubiquitin can be thought of as a kind of \u201ctag\u201d: 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.<\/p>\n\n\n\n

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 \u0110iki\u0107: \u201cHowever, 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.\u201d<\/p>\n\n\n\n

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1 Dr. Adriana Covarrubias Pinto, a postdoctoral researcher in the \u0110iki\u0107 group, at the fluorescence microscope. The cell components, each shown in a different color, can be superimposed. Photo: AG \u0110iki\u0107<\/figcaption><\/figure>\n\n\n\n
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2+3 Two proteins (green and red) form a complex (yellow) during a degradation process in the cell. Normally, these complexes are then transported to the relevant degradation compartment (magenta). In the cell in figure 2, however, the red protein is mutated, which disrupts the degradation pathway and prevents the complexes from reaching the degradative compartment. Blue: cell nucleus.
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 \u0110iki\u0107, 4 Grumati et al. eLife 2017 https:\/\/doi.org\/10.7554\/eLife.25555<\/a>, 5 Dr. Alexandra Hertel<\/figcaption><\/figure>\n\n\n\n
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Forced proximity<\/h3>\n\n\n\n

Proximity-inducing drugs (proxidrugs) facilitate the targeted degradation of specific proteins by the UPS. The idea behind this is actually quite simple, as \u0110iki\u0107 explains: \u201cYou induce the transfer of ubiquitin chains to the target protein and thus mark it for the proteasome shredder.\u201d 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.<\/p>\n\n\n\n

\u201cThe 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,\u201d explains \u0110iki\u0107<\/a>. \u201cToday we know that thalidomide is very effective against multiple myeloma.\u201d Science now has a better understanding of how thalidomide works \u2013 the small molecule binds to an E3 ubiquitin ligase and can, for example, reprogram the ligase\u2019s 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.<\/p>\n\n\n\n

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 \u2013 the linker. One of the \u201cbricks\u201d 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 \u2013 an anti-breast cancer that has been tested on patients in phase III trials since 2023.<\/p>\n\n\n\n

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Basis for novel therapies<\/h3>\n\n\n\n
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PhD student Miles Willoughby (l.) and postdoctoral researcher Dr. Ah Jung Heo (r.) in conversation with Professor Ivan \u0110iki\u0107. Photo: Peter Kiefer
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Advancing the development of such compounds is the goal of the PROXIDRUGS cluster coordinated by Ivan \u0110iki\u0107 (see box). \u201cThe idea is to bring together experts from the Rhine-Main region and beyond to functionalize the ubiquitin system for the development of new drugs,\u201d says \u0110iki\u0107. \u201cWe 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.\u201d This also includes finding ways of delivering proxidrugs to their respective target sites, for example the brain or other organs.<\/p>\n\n\n\n

Among other things, the researchers are endeavoring to make better use of the natural diversity of E3 ubiquitin ligases, as \u0110iki\u0107 explains: \u201cOf the more than 600 variants that occur in human cells, we currently use mainly two.\u201d 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. \u201cBut the ligases we use are also active in healthy cells,\u201d notes \u0110iki\u0107, \u201cmeaning that a PROTAC can trigger undesirable effects.\u201d It would therefore be better to use a ligase that is significantly more active in the target tissue \u2013 for example in certain cancer cells \u2013 than in healthy cells.<\/p>\n\n\n\n

The instruments and technologies used in the search for suitable PROTAC candidates have been bundled within the \u201cFrankfurt Competence Center for Emerging Therapeutics (FCET)\u201d. FCET was founded as a competence center within the framework of the \u201cGoethe Center for (High) Technology (Go4Tec)\u201d. According to \u0110iki\u0107, FCET provides everything needed from the design of active compounds to their validation in animal models. \u201cOur culture of interdisciplinarity and teamwork is the key to our success,\u201d emphasizes the biochemist. \u201cIt is this exchange across scientific disciplines that makes our work truly efficient.\u201d \u0110iki\u0107 is already dreaming of expanding the PROXIDRUGS cluster even further in the second funding phase: \u201cWe 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.\u201d<\/p>\n\n\n\n

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Proxidrugs<\/strong> \/ Degradation of target structures as a novel mode of action for drugs Researchers in the Cluster4Future PROXIDRUGS<\/a> are developing novel drugs \u2013 so-called proximity-inducing drugs (proxidrugs) \u2013 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 \u0110iki\u0107 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 \u20ac14 million within the Clusters4Future initiative of the Federal Ministry of Education and Research (BMBF). In 2024, PROXIDRUGS was able to raise up to \u20ac15 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.<\/p>\n\n\n\n

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About \/ Ivan \u0110iki\u0107<\/strong>, 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), \u0110iki\u0107 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<\/a><\/p>\n\n\n\n

\"Larissa
Photo: Wolfgang Zwanzger<\/figcaption><\/figure>\n\n\n\n

The author \/ Larissa Tetsch<\/strong> 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 \u201cBiologie in unserer Zeit<\/em>\u201d.<\/p>\n\n\n\n

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Futher issues of Forschung Fankfurt<\/a><\/p>","protected":false},"excerpt":{"rendered":"

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 \u2013 nomen est omen \u2013 […]<\/p>\n","protected":false},"author":8,"featured_media":83097,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_eb_attr":"","_price":"","_stock":"","_tribe_ticket_header":"","_tribe_default_ticket_provider":"","_ticket_start_date":"","_ticket_end_date":"","_tribe_ticket_show_description":"","_tribe_ticket_show_not_going":false,"_tribe_ticket_use_global_stock":"","_tribe_ticket_global_stock_level":"","_global_stock_mode":"","_global_stock_cap":"","_tribe_rsvp_for_event":"","_tribe_ticket_going_count":"","_tribe_ticket_not_going_count":"","_tribe_tickets_list":"[]","_tribe_ticket_has_attendee_info_fields":false,"footnotes":""},"categories":[126,254],"tags":[399,247],"post_folder":[],"class_list":["post-83532","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-english","category-research","tag-forschung-frankfurt-1-24","tag-medicine"],"yoast_head":"\nTargeted removal of disease triggers | Aktuelles aus der Goethe-Universit\u00e4t Frankfurt<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/aktuelles.uni-frankfurt.de\/en\/english\/targeted-removal-of-disease-triggers\/\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Targeted removal of disease triggers | Aktuelles aus der Goethe-Universit\u00e4t Frankfurt\" \/>\n<meta property=\"og:description\" content=\"How reprogramming cells can degrade harmful proteins and combat diseases Ubiquitin is a small protein present in the cells of almost all organisms. 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