M. Bermúdez
@bermudez-lab.bsky.social
Münster | Scientist | Computer-Aided Drug Design | GPCRs | In-Silico Pharmacology
Different agonists activate the receptor through specific activation trajectories. We demonstrate this effect in living cells with a novel type of biosensor. www.nature.com/articles/s41...
Ligand-specific activation trajectories dictate GPCR signalling in cells - Nature
Different agonists produce equilibria of at least four distinct active states of the G-protein-bound M2 muscarinic acetylcholine receptor, each with a different ability to activate G proteins.
nature.com
In our novel study, we report well-validated models for opioid peptide binding at the atypical chemokine receptor 3 to understand their ligand promiscuity and to provide starting points for structure-based drug design. #compchem pubs.acs.org/doi/full/10....
Deciphering Opioid Peptide Binding Modes at Atypical Chemokine Receptor 3
ACKR3 is a class A G protein-coupled receptor that is considered as an atypical chemokine receptor. It does not activate G proteins but efficiently recruits β-arrestin and mediates ligand internalizat...
pubs.acs.org
New Preprint alert! Dynamics of Ligand Binding Sites and Chloride Penetration in a Bitter Taste GPCR, with Alon Rainish and Liel Sapir lnkd.in/eXd4hUw8
Congratulations to Dmitrii Kalinin, Verena Spiegler, and Diddo Diddens who officially completed their habilitation procedures @uni-muenster.de this month. Thank you for your inspiring inaugural lectures! (Photos: Uni MS - Hauke Engler, Alina Siutkina)
Here, we present MDPath, a novel tool to study allosteric communication pathways within protein structures: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations. pubs.acs.org/doi/10.1021/...
MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations
Understanding allosteric communication in proteins remains a critical challenge for structure-based, rational drug design. We present MDPath, a Python toolkit for analyzing allosteric communication paths in molecular dynamics simulations using NMI-based analysis. We demonstrate MDPath’s ability to identify both established and novel GPCR allosteric mechanisms using the β2-adrenoceptor, adenosine A2A receptor, and μ-opioid receptor as model systems. The toolkit reveals ligand-specific allosteric effects in β2-adrenoceptor and MOR, illustrating how protein–ligand interactions drive conformational changes. Analysis of ABL1 kinase in complex with allosteric and orthosteric inhibitors demonstrates the broader applicability of the approach. Ultimately, MDPath provides an open-source framework for mapping allosteric communication within proteins, advancing structure-based drug design (https://github.com/wolberlab/mdpath).
pubs.acs.org
It is a great pleasure to share that our extensive review on "The Chemistry and Biology of the Tetrodotoxin Natural Product Family" has been accepted for publication at Angewandte Chemie: doi.org/10.1002/anie....
📣 We are hiring a PhD candidate in computer-aided drug design with passion for MD simulations and ion channels to join our enthusiastic team at the University of Münster. For more details and information how to apply, please visit: uni.ms/j49p2
Doctoral Research Associate Wissenschaftliche*r Mitarbeiter*in (salary level E 13 TV-L, 65%)
uni.ms