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Köhn Group

Phosphatase chemistry and biology

Figure 2: Solid phase synthesis of phosphoinositides for the preparation of libraries to enable SAR studies with lipid phosphatases. (B) A selective activator of PP1 in cells (collaboration with the Hart team and Bollen (KU Leuven) group)

Figure 1: (A) Solid phase synthesis of phosphoinositides for the preparation of libraries for SAR studies with lipid phosphatases (Bru et al., Chem. Sci. 2012). (B) Selective activators of PP1 in cells enable us to gain new insights into PP1 biology (Angew. Chem. Int. Ed. 2012, Chem. Biol. 2013)

Figure 2: DEPOD, the human dephosphorylation database (Li et al., 2013) – see www.depod.org

Figure 2: DEPOD, the human dephosphorylation database (Li et al., 2013)

The Köhn group combines molecular biology, biochemistry and synthetic chemistry to develop new approaches to study phosphatases, which can play a major role in cancer.

Previous and current research

Within intracellular signalling networks, phosphatases are counter players of kinases and play crucial roles in health and disease. The investigation of phosphatases is challenging, which is also due to the lack of tools to selectively study particular phosphatases. Understanding of phosphatase function, regulation and substrate interaction is therefore still quite limited. Our main interest is thus to control and investigate phosphatases using interdisciplinary approaches.

Specifically, we are interested in the phosphatase of regenerating liver (PRL) enzymes, in particular PRL-3. We study biological pathways and roles of this family using biochemical and molecular cell biology approaches, and we aim to design inhibitors for PRL members. We have observed phosphoinositide-phosphatase activity in vitro for one member, PRL-3 (McParland et al., 2011). In this regard, we developed a solid phase synthesis strategy that accelerates access to phosphoinositides and their analogues (figure 1a, Bru et al., 2012). We aim to obtain a detailed picture of substrate specificities of lipid phosphatases in biochemical structure–activity relationship (SAR) studies using a library of phosphoinositide analogues to support designing specific inhibitors of lipid phosphatases.

Another interest is the tool development for protein phosphatase-1 (PP1), a ubiquitous phosphatase that is responsible for a majority of all dephosphorylation reactions on Ser/Thr inside cells and is involved in many processes such as mitosis and cell cycle regulation. We have developed a selective peptide-based PP1 activator (figure 1b), which is an enabling tool to gain novel insights into PP1 biology (Chatterjee et al., Angew. Chem. Int. Ed. 2012). We follow up several strategies for the refinement of this activator and for the development of further PP1-directed chemical tools.

To support the research on phosphatase-kinase-substrate networks, in collaboration with the Wilmanns and Thornton groups, we have created the human DEPhOsphorylation Database: DEPOD (figure 2). We have applied DEPOD data to re-classify the human phosphatome and to analyse phosphatase substrate specificities and their relation to kinases (Li et al., Sci. Signal. 2013).

Future projects and goals

Studying PRL biology will remain a focus of the laboratory in the future, with the aim to understand the underlying mechanisms of oncogenesis caused by these phosphatases. We continue to develop chemical methods to enable applying peptides and inositides as phosphatase modulators inside cells. Designing modulators for the highly complex serine/threonine phosphatases is another long-term goal. Furthermore, we will continue to develop, extend and maintain DEPOD.

The lab consists of an equal number of molecular biologists and organic chemists on the graduate student and postdoctoral level. The combination of biology and chemistry not only opens up new ways to approach the challenging phosphatase research, but also broadens views and skills of every lab member.

Chemistry at EMBL