Life Sciences - Groups

Kassel-Schwiete Research Group: Development of Pharmacological Probes

Sebastian Thallmeier

Nowadays, computational modeling and theoretical methods are an important, indispensable aspect in life sciences aiming at more and more reliable modeling of more and more complex systems. Our group uses methods which work at different spatial and temporal resolution. For one thing, we apply quantum chemical methods which are based on the calculation of the wave function of the electron cloud around the classical nuclei. Secondly, we apply classical molecular dynamics with different resolutions. For the finer atomistic resolution, every atom is modeled as one particle. In contrast, atoms are grouped together in coarse-grained simulations. This simplifies the considered molecules and enables longer simulations of larger (bio)molecular systems. In general, more accurate methods require a larger computing effort. Thus, their application is limited to shorter processes and smaller systems.

The thematic focus of our group is in the fields of biophysics and medicinal chemistry. In particular, we are working on the development and characterization of pharmacological probes. Thereby, the investigation of the interactions between proteins and small molecules is crucial. Often, the small molecules interact only with one or a small group of proteins. Firstly, we aim at understanding why a molecule interacts strongly with certain proteins and not with others. Based thereon, we can alter the molecule in a defined way to strengthen the desired interaction. The goal is to develop molecules favorably interacting with specific proteins that play a role in diseases. The resulting pharmacologically active molecules can be experimentally synthesized, tested, and further improved. Thus, our research can contribute to the development of new medicines.

You can find further research topics, our scientific publications, as well as our engagement in public outreach on the pages Research and Publications. In the following, you can read the latest news from our group.

Fellow Detail

Research and Publications

News

07.09.2021 — The Martini Workshop marked the beginning of a month with multiple presentations about our research. Sebastian Thallmair will give an invited lecture at the CLiC Conference. Moreover, he will present the research group at the PhD Days of the FIAS and give a talk at the virtual autumn meeting of the German Physical Society.

03.09.2021 — Today, the three-day online Martini Workshop ended successfully. It included tutorials, recorded lectures, as well as corresponding Q&A sessions which were provided live. Sebastian Thallmair presented the protein models in Martini 3 in an invited talk and supervised the protein tutorials. Cristina Gil Herrero participated at the workshop as well.

17.08.2021 — When simulating lipid bilayers with cholesterol, artificial temperature gradients can build up which impact membrane properties. Together with researchers at the Czech Academy of Sciences and the University of Groningen, we found out that this issue occurs in coarse-grained as well as atomistic simulations. In our recent publication in The Journal of Physical Chemistry B we discuss how these artifacts can be avoided.

16.08.2021 — Our protein engineering study of an ω-transaminase in collaboration with researchers at the University of Groningen is now published in ACS Catalysis. We used a computational design protocol to increase the substrate scope of the thermostable, synthetically attractive transaminase and verified the results experimentally.

02.08.2021 — Welcome Cristina Gil Herrero! Cristina, who did her Master studies in Theoretical Chemistry and Computational Modeling at the Autonomous University of Madrid, joins us for her PhD to work on protein-ligand interactions.

12.07.2021 — We happily welcome Timo Bachmann from the University of Vienna in the Thallmair Group! He will do a research internship in the framework of an Erasmus+ fellowship.

09.07.2021 — Today's online mini-symposium comprised contributions by the four CMMS junior groups as well as additional junior groups from the Rhein-Main area. The mini-symposium which was initiated by Roberto Covino and Sebastian Thallmair included seven exciting presentations in the field of modeling and computational biology.

16.06.2021 — An online Martini workshop will take place from 1-3 September 2021. The focus of the three-day workshop will be on the new version of the coarse-grained force field, Martini 3. There will be lectures by the key developers as well as supervised tutorial sessions. Sebastian Thallmair will present a lecture as well. More information and a link for registration are available here.

29.03.2021 — The eagarly awaited and completely reparametrized version of the coarse-grained force field Martini 3 is now published after countless iterations of optimizations. The publication entitled "Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics" is published in Nature Methods. All details and the vast collection of test systems are discussed in the 116 (!) pages of supporting information. The force field parameters can be downloaded here.

18.03.2021 — Starting from sulfonamide inhibitors, we developed two light-switchable inhibitors in collaboration with researchers at the University of Groningen and the University Medical Center Groningen. You can read more about it in our publication "Biaryl Sulfonamides as cisoid Azosteres for Photopharmacology" published in Chemical Communications.

03.03.2021 — The Thallmair Group is one of the four young research groups established at the FIAS within the CMMS project in 2020. If you would like to know more about the four groups, please enjoy our short movie. It was prepared in the framework of the "Giersch - Summerschool & International Conference".

05.02.2021 — We offer a PhD position in "Microscopic Modeling of Protein-Drug Binding" and look forward to receiving your application before 28.02.2021. More information is provided in the job advertisement.

27.01.2021 — The editors of Nature Communications feature our article "Protein-ligand binding with the coarse-grained Martini model" in the Editor's Highlights on the topic "Structural biology, biochemistry and biophysics". Thanks and congratulations to all coauthors from Groningen, Lugano, Lyon and Chicago!

01.01.2021 — The Thallmair Group wishes a Happy New Year!

10.12.2020 — It has been a while since Sebastian Thallmair worked experimentally in a chemistry lab. Some of his work on synthesis and characterization of Fe(II) spin-crossover complexes appeared now in the Journal of Inorganic and General Chemistry.

Members

Cristina Gil Herrero

Cristina Gil Herrero

PhD Student

Office: 1|302 (FIAS)
Phone: +49 69 798 47608

Timo Bachmann

Timo Bachmann

Master Student

Office: 1|302 (FIAS)
Phone: +49 69 798 47608