Project
AA1-15
Math-Powered Drug-Design
Project Heads
Konstantin Fackeldey, Christof Schütte, Vikram Sunkara, Christoph Stein, Marcus Weber, Stefanie Winkelmann
Project Members
Luca Donati, Christopher Secker, Celvic Coomber
Project Duration
01.04.2022 − 31.03.2025
Located at
TU Berlin, ZIB
Description
This project aims to propose a new drug design strategy for G-protein coupled receptors by distinguishing between the effects of drugs in healthy and pathological environment. It extends previous projects by (I) coupling the molecular timescales of receptor activation with the associated cellular processes and the adverse side effects induced by them, and by (II) generalizing the new strategy beyond opioid receptors and pain relief towards the treatment of e.g. blood pressure, heart failure, or respiratory failure (e.g. Covid-19).
Project Webpages
There is a ZIB webpage about this project here.
Related Publications
- A. Sikorski, A. Niknejad, M. Weber, L. Donati. Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies. The Journal of Chemical Physics, 160(10), 2024. DOI
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L. Donati, K. Fackeldey, M. Weber. Augmented ant colony algorithm for virtual drug discovery. Journal of Mathematical Chemistry, 62(2), 2024. DOI
- A. Montefusco, L. Helfmann, T. Okunola, S. Winkelmann, C. Schütte. Partial mean-field model for neurotransmission dynamics. Mathematical Biosciences, 369, 2024. DOI
- L. Donati, K. Fackeldey, and M. Weber. In: Swarm Intell., 2023, Under review. DOI
- R. Erban, S. Winkelmann. Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling, 2024. Under review. DOI
- S. Ray, K. Fackeldey, C. Stein, M. Weber. Coarse-Grained MD Simulations of Opioid Interactions with the μ-Opioid Receptor and the Surrounding Lipid Membrane. Biophysica, 3(2), 2023. DOI
- L. Donati, M. Weber. Efficient estimation of transition rates as functions of pH. PAMM, 23(4), 2023. DOI
- A. Thies, V. Sunkara, S. Ray, H. Wulkow, M. Ö. Celik, F. Yergöz, C. Schütte, C. Stein, M. Weber, S. Winkelmann. Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design. Scientific Reports, 13(1), 2023. DOI
- L. Donati, M. Weber. Assessing transition rates as functions of environmental variables. The Journal of Chemical Physics, 157(22), 2022. DOI
- L. Donati, M. Weber, M. B. G. Keller. A review of Girsanov reweighting and of square root approximation for building molecular Markov state models. Journal of Mathematical Physics, 63(12), 2022. DOI
- H. H. Boltz, A. Sirbu, N. Stelzer, P. de Lanerolle, S. Winkelmann, and P. Annibale. The impact of membrane protein diffusion on GPCR signaling. Cells, 11(10), 2022. DOI
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