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2,012 results for “kinase”
Relapsing Forms of Multiple Sclerosis (RMS) Study of Bruton's Tyrosine Kinase (BTK) Inhibitor Tolebrutinib (SAR442168) (GEMINI 1)
ClinicalTrials.gov study NCT04410978. IPD Sharing: YES. Countries: 24. Publications: 1.
Nonrelapsing Secondary Progressive Multiple Sclerosis (NRSPMS) Study of Bruton's Tyrosine Kinase (BTK) Inhibitor Tolebrutinib (SAR442168) (HERCULES)
ClinicalTrials.gov study NCT04411641. IPD Sharing: YES. Countries: 31. Publications: 1.
Relapsing Forms of Multiple Sclerosis (RMS) Study of Bruton's Tyrosine Kinase (BTK) Inhibitor Tolebrutinib (SAR442168) (GEMINI 2)
ClinicalTrials.gov study NCT04410991. IPD Sharing: YES. Countries: 28. Publications: 1.
Study of Selective BRAF Kinase Inhibitor Dabrafenib Monotherapy Twice Daily and in Combination With Dabrafenib Twice Daily and Trametinib Once Daily in Combination Therapy in Subjects With BRAF V600E
ClinicalTrials.gov study NCT01336634. IPD Sharing: YES. Countries: 11. Publications: 5.
A Study of Brigatinib in Participants With Anaplastic Lymphoma Kinase-Positive (ALK+), Advanced Non-Small-Cell Lung Cancer (NSCLC) Progressed on Alectinib or Ceritinib
ClinicalTrials.gov study NCT03535740. IPD Sharing: YES. Countries: 15. Publications: 3.
Data for: High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display
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The kinase ERK plays a conserved dominant role in the heterogeneity of epithelial-mesenchymal transition in pancreatic cancer cells
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Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2: Part 1
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Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2: Part 2
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Stimulation of the catalytic activity of the tyrosine kinase Btk by the adaptor protein Grb2: Part 3
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Supplementary information to the article by van Beijnum et al. "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment"
<p>Supplementary information to the article "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment".</p> <p><strong>Judy R. van Beijnum<sup>1</sup>, Andrea Weiss<sup>2, 3</sup>, Robert H. Berndsen<sup>1,2 </sup>, Tse J. Wong<sup>1</sup>, Louise C. Reckman<sup>1</sup>, Sander R. Piersma<sup>4,5</sup>, Marloes Zoetemelk<sup>2,3</sup>, Richard de Haas<sup>1,4,5</sup>, Olivier Dormond<sup>6</sup>, Axel Bex<sup>7,8</sup>, Alexander A. Henneman<sup>4,5</sup>, Connie R. Jimenez<sup>4,5</sup>, Arjan W. Griffioen<sup>1</sup>, Patrycja Nowak-Sliwinska<sup>2,3,9</sup>*</strong></p> <p> </p> <p><sup>1</sup> Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands;</p> <p><sup>2</sup> Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland*;</p> <p><sup>3 </sup>Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland</p> <p><sup>4 </sup>Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands</p> <p><sup>5</sup> OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands</p> <p><sup>6</sup> Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland<sup> </sup> </p> <p><sup>7</sup> Royal Free London NHS Foundation Trust, Renal Cancer Centre, UCL Division of Surgical and Interventional Science, London, UK</p> <p><sup>8</sup> Netherlands Cancer Institute, Amsterdam, The Netherlands</p> <p><sup>9 </sup> Translational Research Centre in Oncohaematology, Geneva, Switzerland</p> <p> Correspondence: <a href="mailto:Patrycja.Nowak-Sliwinska@unige.ch">Patrycja.Nowak-Sliwinska@unige.ch</a></p>
Human Receptor-Interacting Serine/Threonine-Protein Kinase 2 (RIPK2); A Target Enabling Package
<p>RIPK2 inflammatory signalling downstream from the bacteria-sensing receptors NOD1 and NOD2 is associated with auto-immune and inflammatory conditions. RIPK2 inhibition has shown promise in disease models of inflammatory bowel disease and multiple sclerosis. In this TEP, we reveal a lack of correlation between inhibitor efficacy in cells and their potency using in vitro kinase assays. We show that RIPK2 kinase activity is in fact dispensable for NOD2 inflammatory signalling and that RIPK2 inhibitors function instead by antagonizing XIAP-binding and ubiquitination of RIPK2. We characterise the molecular basis for this effect. We also solved the first crystal structure of the RIPK2 kinase domain and applied a range of biochemical and cellular assays to profile type I and type II RIPK2 kinase inhibitors. Overall, our study illustrates how to target the ATP-binding pocket in RIPK2 to interfere with the RIPK2-XIAP interaction for modulation of NOD signalling.</p>
Human LIM domain kinase 1 (LIMK1), kinase domain; A Target Enabling Package
<p>Loss of the translational repressor FMRP in fragile X syndrome causes upregulation of the type II BMP receptor BMPR2 and its non-canonical signalling via the kinase LIMK1. LIMK1 performs inhibitory phosphorylation on cofilin proteins blocking their actin-severing activity. Excessive BMPR2-LIMK1 activation was associated with dendritic spine and behavioural defects in animal models that could be rescued by BMPR2 knockdown or LIMK1 inhibition. Here we present a target enabling package for the therapeutic target LIMK1. We include crystal structures of BMPR2, LIMK1, LIMK2 and the LIMK1-cofilin complex, as well as multiple assays for small molecule inhibitor screening. Finally, we identify a series of allosteric LIMK1 inhibitors with promising potency and selectivity that may potentially allow the development of a safe drug for this chronic indication.</p>
Different types of kinase inhibitors with experimentally confirmed mechanism of action
<p>A data set of ATP-competitive and allosteric inhibitors of human protein kinases with mechanisms of action confirmed by X-ray crystallography is provided. Data were acquired from the Protein Data Bank (PDB) and the KLIFS, ProfKin, ASD, and ChEMBL databases, curated, and organized. The composition of the data set is detailed in the accompanying readme.txt file.</p> <p> </p> <p> </p>
A Set of 72 Kinase Inhibitors
<p>A set of 72 known kinase inhibitors was assembled from ChEMBL release 18. For each inhibitor, MACCS and ECFP4 representations are provided. Both fingerprints were calculated using an in-house implementation based upon OpenEye's OEChem toolkit. For MACCS, we used SMARTS patterns adapted from RDKit.</p>
KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space
<p>The Kinase-Ligand Interaction Fingerprints and Structure database (KLIFS) contains a consistent structural alignment and deconstruction of the kinase domains from over 1734 PDB structures covering 190 different human kinases. </p> <p>Every crystal structure was structurally aligned in a consistent manner, subsequently broken down from the full complex into separate structural parts: the protein, the orthosteric ligand-binding pocket (85 aligned residues covering the catalytic cleft), orthosteric and allosteric ligand(s), ions, organometallics, cofactors, and waters. By combining the pocket with the orthosteric ligand all interactions are annotated using Interactions FingerPrints (IFPs) for systematic comparison.</p>
Molecular Dynamics Simulations and associated data for: Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases
<p>Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The Doublecortin Like Kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other Calcium Calmodulin Kinases (CAMKs), and a 'Swiss-army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for auto-regulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor-binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome–wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically-divergent DCLK1 modulators, stabilizers or degraders.</p>
A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells
<p>Annotated WES VCF file and phenotype file used in Gene burden analysis of Naaldijk et al., "A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells", 2023. </p><p> </p>
Data from: Myristoyl's dual role in allosterically regulating and localizing Abl kinase
<p>c-Abl kinase, a key signalling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl-modification can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the auto-inhibitory assembly. Activation is triggered by myristoyl release. We used molecular dynamics simulations to show how both myristoyl and the Src homology domains are required to impose the full inhibitory effect on the kinase domain, and reveal the allosteric transmission pathway at residue-level resolution. Importantly, we find myristoyl insertion into a membrane to thermodynamically compete with binding to c-Abl. Myristoyl thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its pre-activated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.</p>
AlphaFold Structures for: A wheat tandem kinase activates an NLR to trigger immunity
<p>AlphaFold Predictions used for analysis in "A wheat tandem kinase activates an NLR to trigger immunity".</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.