Position: Scientific Researcher

Room no.: CP-02-133

Telephone no.: +49 (0)231 755 8834


Member of the group: since 06/2019


Earlier Positions:

01/2014 – 05/2019
PhD student at the Faculty of Chemistry and Chemical Biology, TU Dortmund University

10/2008 – 12/2013
Bachelor and Master of Science in Biochemistry, Martin-Luther-Universität Halle-Wittenberg

Expertise: Structure-Based Design with Focus on Binding Site
Identification/Characterization/Comparison, MD Simulation Studies, Cheminformatic Analyses

Off-Lab activities (hobbies): Literature, Irish Language, Music

Research projects:
With respect to protein kinase research, it is a major challenge to pool the available knowledge of
bioactivities and selectivities to exploit this data for the rational planning of upcoming steps. The
development of methodologies to analyze structure-activity relationships is crucial for well-characterized
targets. Additionally, docking studies, pharmacophore searches, and MD simulations offer a broader
insight into the field of protein-ligand interactions and kinase conformations.

The establishment of a fragment screening library necessitates the preparation of databases of
commercially available compounds, the in silico generation of synthetically accessible product libraries,
the analysis of the available chemical space, and the rational selection of synthesis candidates. These
major components are to be incorporated in a multi-purpose workflow which enables the analysis of huge
chemical libraries and facilitates multiple steps of fragment development.

Binding Site Analyses

  1. Ehrt, C.; Brinkjost, T.; Koch, O. Impact of binding site comparisons on medicinal chemistry and rational
    molecular design. J. Med. Chem. 2016, 59 (9), 4121–4151.
  2. Ehrt, C.; Brinkjost, T.; Koch, O. A benchmark driven guide to binding site comparison: An exhaustive
    evaluation using tailor-made data sets (ProSPECCTs). PLoS Comput. Biol. 2018, 14 (11), e1006483.
  3. Ehrt, C.; Brinkjost, T.; Koch, O. Binding site characterization - similarity, promiscuity, and druggability.
    MedChemComm 2019, 10 (7), 1145–1159.

MD Simulation Studies

  1. Zhao, L.; Ehrt, C.; Koch, O.; Wu, Y.-W. One-pot N2C/C2C/N2N ligation to trap weak protein-protein
    interactions. Angew. Chem. Int. Ed. Engl. 2016, 55 (28), 8129–8133.
  2. Kaitsiotou, H.; Keul, M.; Hardick, J.; Mühlenberg, T.; Ketzer, J.; Ehrt, C.; Krüll, J.; Medda, F.; Koch, O.;
    Giordanetto, F.; Bauer, S.; Rauh, D. Inhibitors to overcome secondary mutations in the stem cell factor
    receptor KIT. J. Med. Chem. 2017, 60 (21), 8801–8815.
  3. Maurer, S.; Buchmuller, B.; Ehrt, C.; Jasper, J.; Koch, O.; Summerer, D. Overcoming conservation in
    TALE-DNA interactions: a minimal repeat scaffold enables selective recognition of an oxidized 5-
    methylcytosine. Chem. Sci. 2018, 9 (36), 7247–7252.
  4. Seifert, S.; Ehrt, C.; Lückfeldt, L.; Lubeck, M.; Schramm, F.; Brakmann, S. Optical control of
    transcription - genetically encoded photoswitchable variants of T7 RNA polymerase. ChemBioChem