Biology subjects

Gossen, J.

Publications and source records attributed to Gossen, J..

5 recordsLinked to original sources

bioRxiv2024

KIRA6 is an effective and versatile mast cell inhibitor of IgE-mediated activation

Incidents of IgE-mediated, mast cell (MC)-driven allergic diseases are constantly rising and there is an urgent need for the development of novel pharmacological MC stabilizers. Allergen/antigen (Ag)-triggered activation of MCs via crosslinking of the high-affinity receptor for IgE (Fc{varepsilon}RI) is regulated, amongst others, by the coordinated action of various cytosolic tyrosine kinases of the SRC family, e.g. LYN and FYN, which exert positive as well as negative functions. We report that KIRA6, an inhibitor developed for the endoplasmic reticulum (ER) stress sensor IRE1, suppresses IgE-mediated pro-inflammatory MC activation by inhibiting both LYN and FYN. KIRA6 dose-dependently and effectively attenuates Ag-stimulated early signaling (e.g. substrate tyrosine phosphorylation, Ca2+ mobilization, and activation of MAPK pathways) as well as effector functions such as degranulation and pro-inflammatory cytokine production/secretion in murine bone marrow-derived MCs (BMMCs). Moreover, Ag-triggered bronchoconstriction in an ex vivo model of precision-cut lung slices (PCLS), and IgE-mediated stimulation of human MCs were repressed by KIRA6. To get in-depth inside into KIRA6 interaction with three MC-relevant tyrosine kinases, LYN, FYN, and KIT, and to elicit the potential of KIRA6 structure to serve as pharmacophore for the development of respective single-, dual-, or triple-specificity inhibitors, we modeled and evaluated the binding of KIRA6 on the three kinases by applying homology modeling and molecular dynamics simulations, as well as MM GBSA calculations. We found that KIRA6 has a high propensity to bind the inactive state of LYN, FYN, and KIT with comparable affinities. In conclusion, our data suggest the use of novel inhibitors based on the KIRA6 pharmacophore as effective MC stabilizers to improve treatment of pro-inflammatory diseases with MC involvement in need of effective pharmacological interventions.

immunology↗

bioRxiv2023

AI-based novel-chemotype GPCRs drugs: introducing ligand type classifiers and systems biology

Identifying the correct chemotype of ligands targeting receptors (i.e., agonist or antagonist) is a challenge for in silico screening campaigns. Here we present an approach that identifies novel chemotype ligands by combining structural data with a random forest agonist/antagonist classifier and a signal-transduction kinetic model. As a test case, we apply this approach to identify novel antagonists of the human adenosine transmembrane receptor type 2A, an attractive target against Parkinsons disease and cancer. The identified antagonists were tested here in a radioligand binding assay. Among those, we found a promising ligand whose chemotype differs significantly from all so-far reported antagonists, with a binding affinity of 310{+/-}23.4 nM. Thus, our protocol emerges as a powerful approach to identify promising ligand candidates with novel chemotypes while preserving antagonistic potential and affinity in the nanomolar range.

bioinformatics↗

bioRxiv2022

SSB toolkit: from molecular structure to subcellular signaling pathways.

We present, here, an open-source systems biology toolkit to simulate mathematical models of the signal-transduction pathways of G-protein coupled receptors (GPCRs). By merging structural macromolecular data with systems biology simulations, we developed a framework to simulate the signal-transduction kinetics induced by ligand-GPCR interactions, as well as the consequent change of concentration of signaling molecular species, as a function of time and ligand concentration. Therefore, this tool brings to the light the possibility to investigate the subcellular effects of ligand binding upon receptor activation, deepening the understanding of the relationship between the molecular level of ligand-target interactions and higher-level cellular and physiologic or pathological response mechanisms.

bioinformatics↗

bioRxiv2020

Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in-vitro repurposing screen

Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro, and have identified 62 additional compounds with IC50 values below 1 M and profiled their selectivity towards Chymotrypsin and 3CL-Pro from the MERS virus. A subset of 8 inhibitors showed anti-cytopathic effect in a Vero-E6 cell line and the compounds thioguanosine and MG-132 were analysed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 [A], showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/422677v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17ca2aeorg.highwire.dtl.DTLVardef@19c5159org.highwire.dtl.DTLVardef@1a0adf6org.highwire.dtl.DTLVardef@1fd05cd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOAbstract Figure.C_FLOATNO Workflow for identification and profiling of inhibitors of SARS-CoV-2 3CL-Pro using a large scale repurposing and bioactive compound collection (rhs). Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray. C_FIG

molecular biology↗

bioRxiv2020

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unfortunately, unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of ~30,000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing ~200 virtual screenings of compound libraries on selected protein structures, we redefine the proteins druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites.

biophysics↗