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Targeted Protein Degradation

Our methodological framework combines advanced live-cell imaging with phenotypic, functional, and biochemical protein–protein interaction assays. Complemented by nanobody-based probes and switchable chemical modulators, this interdisciplinary approach allows us to investigate protein function across different spatial and temporal scales. Looking ahead, we see nanobodies and TPD technologies as central elements of next-generation precision therapies. By bridging fundamental cell biology with translational applications, our work aims to provide new avenues for highly specific interventions in oncology and other biomedical fields.

Our research focuses on developing nanobody-based strategies and targeted protein degradation (TPD) technologies to understand and manipulate cellular processes with high precision. Nanobodies, derived from camelid heavy-chain antibodies, are small, stable, and highly specific binders that can penetrate cells and access compartments inaccessible to conventional antibodies. We exploit these properties to generate nanobodies that act as inhibitors, biosensors, or recruiters of degradation machinery, thereby allowing the selective modulation or removal of proteins directly at their site of action.

By integrating nanobody engineering with innovative delivery systems, protein localization signals, and chemical biology approaches, we aim to establish new strategies for both reversible protein interference and acute protein depletion. In this context, we also develop and apply proteolysis-targeting chimeras (PROTACs), which redirect the cell’s degradation machinery toward selected targets. These tools provide unique opportunities to study protein function in real time and to dissect dynamic signaling pathways, while also offering translational potential for targets traditionally considered “undruggable.

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Survivin/1E31 © AG Knauer​

Due to its dual role as an apoptosis inhibitor and mitotic regulator, Survivin is accepted as a nodal protein hub, with high relevance in basic cell and translational cancer biology. Particularly, our work on the impact of Survivin's nuclear export signal not only resulted in several publications but also provided the basis for innovative chemico-genetic translational interference strategies. Currently, we are pursuing the concept of supramolecular inhibition by rational chemical design and specific nanobodies combined with innovative nanocarrier based delivery tools. In addition, we recently revealed a so far unknown role in the DNA damage response and as such now set the stage for in-depth investigations of Survivin's role in cancer biology and therapy response. We additionally focus on Survivin’s apoptotic/mitotic switch, whether it really exists as proposed and how it can be induced. This has so far eluded experimental investigation, although it would be of utmost importance to finally understand how Survivin decides between its different biological roles. 

Although less is known about the molecular (patho)mechanisms of the threonine protease Taspase1, the ZMB’s outstanding expertise in protease research represents an ideal platform to study its unresolved impact on ‘Cell fate decisions in development and disease’. Employing cutting-edge live cell microscopy (in cooperation with our high-end microscopes implemented at the Imaging Center Campus Essen) and biosensor systems, we not only uncovered novel mechanisms regulating Taspase1’s structure activity relationships (SAR), but also identified previously unknown targets with cellular functions in e.g., transcriptional regulation and cell differentiation and migration. Hence, Taspase1 also represents an important molecular switch determining cell fate and in addition serves as a valuable model in protease research to unravel novel fine-tuning mechanisms with translational relevance.

Currently, we are pursuing the concept of supramolecular inhibition of pivotal Taspase1 protein interactions. Here, we particularly focus on its Importin-mediated nuclear transport, but also on the interplay of prerequisites for autocatalytic activation of the protease and proteolytic activity in general. Is it possible to interfere with Importin-related nucleolar association and at which steps of the protease activation process? And finally, how is substrate specificity for only one or a certain subset of Taspase1 target(s) achieved and at which developmental stages? Therefore, we are engaging in developing novel nanobodies targeting Taspase1 to allow specific modulation as well as timely induction of targeted protein degradation (TPD).

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Taspase1/2A8J © AG Knauer​

Recently, we succeeded in the development of supramolecular binders blocking the pivotal interaction of Taspase1's nuclear import signal (NLS) with the import receptor Importin α .