Biology subjects

Bermudez, M.

Publications and source records attributed to Bermudez, M..

7 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of apo human Factor XIa reveal catalytic-domain flexibility and exposure of the Factor IX-binding site

Factor XI (FXI) is a key coagulation protease of the intrinsic pathway of blood coagulation and an emerging antithrombotic target. However, the structural transition from zymogen to active Factor XIa (FXIa) has remained poorly understood. Using cryo-EM, we demonstrate that FXI activation results in a global reorganization of the homodimer, extending beyond the activation loop to include a significant reorientation of the catalytic domain (CD) relative to the apple-domain (AD) platform. The CD displays pronounced conformational heterogeneity; we identify three distinct conformers, suggesting that FXIa exists as a dynamic ensemble rather than a single rigid state. MD analysis indicates that activation disrupts the inter-CD allosteric communication present in the zymogen, thereby facilitating this flexibility. CD plasticity allows for the dynamic exposure of the A3 exosite, facilitating the binding of Factor IX. Comparison with plasma kallikrein (PKa) suggests that such structural flexibility may be a shared feature of apple-domain-containing contact-system proteases. Our results reveal that FXIa functions as a dynamic ensemble, providing a structural framework for understanding substrate recognition and identifying novel, non-catalytic sites for the development of specific FXIa inhibitors.

biochemistry↗

bioRxiv2025

Divergent Side-Chain Networks of the Mineralocorticoid Receptor Control Mutation-Altered Drug Response

The mineralocorticoid receptor (MR) is a nuclear hormone receptor whose activation depends on ligand-induced conformational changes of the activation function-2, particularly involving helix 12. The rare gain-of-function mutation S810L was reported to alter MR pharmacology by converting classical steroidal antagonists such as spironolactone or eplerenone into agonists. In contrast, the non-steroidal antagonist finerenone has been shown to retain its functionality. However, the mechanistic reason for those ligand-specific effects remains elusive. To uncover the molecular basis for this ligand-specific behavior, we performed molecular dynamics simulations of wild-type and S810L MR bound to eplerenone or finerenone. We combined distance metrics with a residue-centered dynophore analysis and MDPath to track allosteric communication pathways and time-resolved side-chain interactions. In S810L, eplerenone shifts AF-2 side-chain networks toward H12, consistent with an agonist-like topology. Finerenone, by contrast, induces a local H3-H5 compaction around M777-810 yet diverts the AF-2 network away from H12, thereby preserving an antagonist-like topology. These network reallocations are absent in wild-type simulations, indicating a mutation-specific ligand-depending divergence. Together, these findings provide a mechanistic explanation for ligand-specific antagonist resilience in S810L MR and represent an example for structural pharmacogenomic approaches.

pharmacology and toxicology↗

bioRxiv2025

Dynamic pharmacophores unveil binding mode ensembles for classical partial agonists at the M2 receptor

For the prototypic M2 receptor it has been previously demonstrated that dualsteric partial agonists can stabilize both, active and inactive receptor states, but it remains unclear whether orthosteric partial agonists have a similar mechanism. Here, we apply dynamic pharmacophores to unveil binding mode ensembles for classical M2 partial agonists. We report correlations between the spatial distribution of lipophilic contacts and ligand efficacy and demonstrate the applicability of dynamic pharmacophores to analyze subtle binding mode changes.

bioinformatics↗

bioRxiv2025

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 MDPaths ability to identify both established and novel GPCR allosteric mechanisms using the {beta}2-adrenoceptor, adenosine A2A receptor, and {micro}-opioid receptor as model systems. The toolkit reveals ligand-specific allosteric effects in {beta}2-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).

bioinformatics↗

bioRxiv2024

Physiological bias governs neutrophil inflammatory threat perception

Background and PurposeThe functional G protein-coupled receptor (GPCR) signalling unit consists of an agonist acting on a receptor that is coupled to a G protein that transduces the signals to effectors within a complex cellular environment. While much attention is given to GPCR-agonist or GPCR-transducer relationships, the contribution of the cellular environment remains significantly unexplored. Experimental ApproachHere, we juxtaposed the signalling responses triggered by the activation of two GPCR pattern recognition receptors, Formyl peptide receptor 1 and Formyl peptide receptor 2, in a recombinant cell system against their signalling dynamics in the native neutrophilic environment. Key resultsWe observed that agonist activation leads to cell context-dependent substantial differences in the receptor signalling texture. While the impact of receptor activation on de novo cAMP formation varied depending on the cell type, MAPK activation was similar in both systems. This physiological bias was conserved across species. Expression analysis unveiled the absence of the Gi-sensitive adenylyl cyclases ADCY5 and ADCY6 in neutrophils, implying that cAMP de novo synthesis cannot be inhibited by Gi-coupled receptors. The signalling behaviour of the Gi-coupled LTB4 high-affinity receptor BLT1 in neutrophils corroborated our findings. Conclusion and ImplicationsOur data underscore the profound impact of the specific cellular environment on GPCR signalling, causing physiological bias in GPCR signalling, thereby affecting drug efficacy and therapeutic targeting.

systems biology↗

bioRxiv2024

Comparative analysis of Formyl peptide receptor 1 and Formyl peptide receptor 2 reveals shared and preserved signaling profiles

Pattern Recognition Receptors are key in identifying pathogenic or damaged cell-related patterns or molecules. Among these, the closely linked formyl peptide receptors FPR1 and FPR2 are believed to hold pivotal yet differing functions in immune regulation. To address the intriguing question of how these highly related receptors with a shared agonist spectrum play differing roles in modulating inflammation, we analyzed the signaling profile for a panel of FPR agonists in vivo and ex vivo settings. Our analysis uncovered a shared core signature for both FPRs across signaling pathways. Whereas formylated peptides generally acted as potent agonists at FPR1, FPR2 agonists, irrespective of N-terminal formylation, displayed consistently low activity ratios, suggesting an underutilized signaling potential of this receptor. Signaling outcomes were defined by specific agonist-receptor pairings and no receptor-specific signaling texture was identified. Activation of the FPR signaling axis by fMLF in human neutrophils did impact neutrophil survival. Overall, the distinct characteristics underlying inflammatory, anti-inflammatory, or pro-resolving profiles could not be attributed to a specific receptor isoform, signaling pattern, or a particular class of agonists, challenging assumptions about distinct inflammatory profiles linked to specific receptors, signaling patterns, or agonist classes.

pharmacology and toxicology↗

bioRxiv2019

BiasDB: A Comprehensive Database for Biased GPCR Ligands

G protein-coupled receptors transmit signals across membranes via interaction with intracellular binding partners. While there is an imprinted signaling profile for each receptor, biased ligands are able to shift intracellular pathways resulting in different recruitment profiles. We present the first comprehensive database of all literature-known biased ligands as a resource for medicinal chemistry and pharmacology. In addition to careful manual curation, we provide an analysis of the data. BiasDB is available at https://biasdb.drug-design.de/.

pharmacology and toxicology↗